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convertion of a CG membrane to FG one with g_fg2cg
- Stéfane
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8 years 6 months ago - 8 years 6 months ago #5151
by Stéfane
convertion of a CG membrane to FG one with g_fg2cg was created by Stéfane
Dear All,
I am trying to do a CG --> FG transformation of a model of a small thylakoid membrane with the parameters described in the Paper of van Eerden (BBA, 2015, 1848, 1319 - 1330). To do the conversion, I am using"g_fg2cg_g" tool available in the gromacs-3.3.1_rev used in the paper. I used the following command (for the system without water and ions):
gromacs-3.3.1_rev/gmx_rev/bin/g_fg2cg_g -pcg Small_plant_CG_noWater_Ions.top -pfg Small_plant_FG_noWater_Ions.top -c Thylakoide_Membrane_CG_npt2_NoWater_Ions.gro -o Thylakoide_Membrane_FG_npt2_NoWater_Ions.gro -n 0 -wat 1
With this command, I obtain the following output :
################################
WARNING 1 : Overriding Proper Dih. parameters, old: 180 9.35 1 0 0 0 new: OA CH2 CH1 OA 1 0.000 9.50 3 Generated 169 of the 1653 non-bonded parameter combinations Excluding 3 bonded neighbours for PPG 7 Excluding 3 bonded neighbours for PPT 14 Excluding 3 bonded neighbours for PDGDG 7 Excluding 3 bonded neighbours for PDGDT 36 Excluding 3 bonded neighbours for PMGDG 50 Excluding 3 bonded neighbours for PMGDT 7 Excluding 3 bonded neighbours for PSQDG 21 Excluding 3 bonded neighbours for PPG 7 Excluding 3 bonded neighbours for PPT 14 Excluding 3 bonded neighbours for PDGDG 7 Excluding 3 bonded neighbours for PDGDT 36 Excluding 3 bonded neighbours for PMGDG 50 Excluding 3 bonded neighbours for PMGDT 7 Excluding 3 bonded neighbours for PSQDG 21 NOTE: System has non-zero total charge: -8.400007e+01 # G96BONDS: 17496 # G96ANGLES: 20326 # PDIHS: 24280 # IDIHS: 2534 # LJ14: 22496 # DIHRES: 1312 calling cpp... processing topology... Generated 0 of the 780 non-bonded parameter combinations Excluding 1 bonded neighbours for PPG 7 Excluding 1 bonded neighbours for PPT 14 Excluding 1 bonded neighbours for PDGDG 7 Excluding 1 bonded neighbours for PDGDT 36 Excluding 1 bonded neighbours for PMGDG 50 Excluding 1 bonded neighbours for PMGDT 7 Excluding 1 bonded neighbours for PSQDG 21 Excluding 1 bonded neighbours for PPG 7 Excluding 1 bonded neighbours for PPT 14 Excluding 1 bonded neighbours for PDGDG 7 Excluding 1 bonded neighbours for PDGDT 36 Excluding 1 bonded neighbours for PMGDG 50 Excluding 1 bonded neighbours for PMGDT 7 Excluding 1 bonded neighbours for PSQDG 21 NOTE: System has non-zero total charge: -8.400000e+01 Number of fg atoms 17452 Number of cg atoms 3950 Reading frames from gro file 'GRowing Old MAkes el Chrono Sweat', 3950 atoms. Reading frame 0 time 0.000 Back Off! I just backed up Thylakoide_Membrane_FG_npt2_NoWater_Ions.gro to Thylakoide_Membrane_FG_npt2_NoWater_Ions.gro Water rewrited to normal representation ! ############################### a gro file "Thylakoide_Membrane_FG_npt2_NoWater_Ions.gro" is created with 17452 atom lines, but only the first 3950 lines have coordinates different to 0. Note that the starting conformation of the CG bilayer was constructed with insane.py with the *.itp taken from THYLAKOIDS.zip archive downloaded from the Martini website. With this system I can run CG simulations without problems ? Below the the top files I used : ############ Small_plant_CG_noWater_Ions.top ################ #include "./CG_itp_files/martini_v2.1.itp" #include "./CG_itp_files/martini_v2.0_ions.itp" #include "./CG_itp_files/plantmembrane.itp" [ system ] blabah [ molecules ] ;upperleaflet PPG 7 PPT 14 PDGDG 7 PDGDT 36 PMGDG 50 PMGDT 7 PSQDG 21 ; lower leaflet PPG 7 PPT 14 PDGDG 7 PDGDT 36 PMGDG 50 PMGDT 7 PSQDG 21 ############ Small_plant_FG_noWater_Ions.top ################ #include "./forcefield.ff/forcefield.itp" #include "./FG_itp_files/PPG.itp" #include "./FG_itp_files/PPT.itp" #include "./FG_itp_files/PDGDG.itp" #include "./FG_itp_files/PDGDT.itp" #include "./FG_itp_files/PMGDG.itp" #include "./FG_itp_files/PMGDT.itp" #include "./FG_itp_files/PSQDG.itp" [ system ] [ molecules ] PPG 7 PPT 14 PDGDG 7 PDGDT 36 PMGDG 50 PMGDT 7 PSQDG 21 ; upper leaflet PPG 7 PPT 14 PDGDG 7 PDGT 36 PMGDG 50 PMGDT 7 PSQDG 21 ############################################ Could help me to find where is my error? Stéfane[file "./forcefield.ff/ffG53a6bon.itp", line 576]:
Overriding Proper Dih. parameters,
old: 180 9.35 1 0 0 0
new: OA CH2 CH1 OA 1 0.000 9.50 3
Generated 169 of the 1653 non-bonded parameter combinations
Excluding 3 bonded neighbours for PPG 7
Excluding 3 bonded neighbours for PPT 14
Excluding 3 bonded neighbours for PDGDG 7
Excluding 3 bonded neighbours for PDGDT 36
Excluding 3 bonded neighbours for PMGDG 50
Excluding 3 bonded neighbours for PMGDT 7
Excluding 3 bonded neighbours for PSQDG 21
Excluding 3 bonded neighbours for PPG 7
Excluding 3 bonded neighbours for PPT 14
Excluding 3 bonded neighbours for PDGDG 7
Excluding 3 bonded neighbours for PDGDT 36
Excluding 3 bonded neighbours for PMGDG 50
Excluding 3 bonded neighbours for PMGDT 7
Excluding 3 bonded neighbours for PSQDG 21
NOTE:
System has non-zero total charge: -8.400007e+01
# G96BONDS: 17496
# G96ANGLES: 20326
# PDIHS: 24280
# IDIHS: 2534
# LJ14: 22496
# DIHRES: 1312
calling cpp...
processing topology...
Generated 0 of the 780 non-bonded parameter combinations
Excluding 1 bonded neighbours for PPG 7
Excluding 1 bonded neighbours for PPT 14
Excluding 1 bonded neighbours for PDGDG 7
Excluding 1 bonded neighbours for PDGDT 36
Excluding 1 bonded neighbours for PMGDG 50
Excluding 1 bonded neighbours for PMGDT 7
Excluding 1 bonded neighbours for PSQDG 21
Excluding 1 bonded neighbours for PPG 7
Excluding 1 bonded neighbours for PPT 14
Excluding 1 bonded neighbours for PDGDG 7
Excluding 1 bonded neighbours for PDGDT 36
Excluding 1 bonded neighbours for PMGDG 50
Excluding 1 bonded neighbours for PMGDT 7
Excluding 1 bonded neighbours for PSQDG 21
NOTE:
System has non-zero total charge: -8.400000e+01
Number of fg atoms 17452
Number of cg atoms 3950
Reading frames from gro file 'GRowing Old MAkes el Chrono Sweat', 3950 atoms.
Reading frame 0 time 0.000
Back Off! I just backed up Thylakoide_Membrane_FG_npt2_NoWater_Ions.gro to Thylakoide_Membrane_FG_npt2_NoWater_Ions.gro
Water rewrited to normal representation !
###############################
a gro file "Thylakoide_Membrane_FG_npt2_NoWater_Ions.gro" is created with 17452 atom lines, but only the first 3950 lines have coordinates different to 0. Note that the starting conformation of the CG bilayer was constructed with insane.py with the *.itp taken from THYLAKOIDS.zip archive downloaded from the Martini website. With this system I can run CG simulations without problems ?
Below the the top files I used :
############ Small_plant_CG_noWater_Ions.top ################
#include "./CG_itp_files/martini_v2.1.itp"
#include "./CG_itp_files/martini_v2.0_ions.itp"
#include "./CG_itp_files/plantmembrane.itp"
[ system ]
blabah
[ molecules ]
;upperleaflet
PPG 7
PPT 14
PDGDG 7
PDGDT 36
PMGDG 50
PMGDT 7
PSQDG 21
; lower leaflet
PPG 7
PPT 14
PDGDG 7
PDGDT 36
PMGDG 50
PMGDT 7
PSQDG 21
############ Small_plant_FG_noWater_Ions.top ################
#include "./forcefield.ff/forcefield.itp"
#include "./FG_itp_files/PPG.itp"
#include "./FG_itp_files/PPT.itp"
#include "./FG_itp_files/PDGDG.itp"
#include "./FG_itp_files/PDGDT.itp"
#include "./FG_itp_files/PMGDG.itp"
#include "./FG_itp_files/PMGDT.itp"
#include "./FG_itp_files/PSQDG.itp"
[ system ]
[ molecules ]
PPG 7
PPT 14
PDGDG 7
PDGDT 36
PMGDG 50
PMGDT 7
PSQDG 21
; upper leaflet
PPG 7
PPT 14
PDGDG 7
PDGT 36
PMGDG 50
PMGDT 7
PSQDG 21
############################################
Could help me to find where is my error?
Stéfane
I am trying to do a CG --> FG transformation of a model of a small thylakoid membrane with the parameters described in the Paper of van Eerden (BBA, 2015, 1848, 1319 - 1330). To do the conversion, I am using"g_fg2cg_g" tool available in the gromacs-3.3.1_rev used in the paper. I used the following command (for the system without water and ions):
gromacs-3.3.1_rev/gmx_rev/bin/g_fg2cg_g -pcg Small_plant_CG_noWater_Ions.top -pfg Small_plant_FG_noWater_Ions.top -c Thylakoide_Membrane_CG_npt2_NoWater_Ions.gro -o Thylakoide_Membrane_FG_npt2_NoWater_Ions.gro -n 0 -wat 1
With this command, I obtain the following output :
################################
WARNING 1 : Overriding Proper Dih. parameters, old: 180 9.35 1 0 0 0 new: OA CH2 CH1 OA 1 0.000 9.50 3 Generated 169 of the 1653 non-bonded parameter combinations Excluding 3 bonded neighbours for PPG 7 Excluding 3 bonded neighbours for PPT 14 Excluding 3 bonded neighbours for PDGDG 7 Excluding 3 bonded neighbours for PDGDT 36 Excluding 3 bonded neighbours for PMGDG 50 Excluding 3 bonded neighbours for PMGDT 7 Excluding 3 bonded neighbours for PSQDG 21 Excluding 3 bonded neighbours for PPG 7 Excluding 3 bonded neighbours for PPT 14 Excluding 3 bonded neighbours for PDGDG 7 Excluding 3 bonded neighbours for PDGDT 36 Excluding 3 bonded neighbours for PMGDG 50 Excluding 3 bonded neighbours for PMGDT 7 Excluding 3 bonded neighbours for PSQDG 21 NOTE: System has non-zero total charge: -8.400007e+01 # G96BONDS: 17496 # G96ANGLES: 20326 # PDIHS: 24280 # IDIHS: 2534 # LJ14: 22496 # DIHRES: 1312 calling cpp... processing topology... Generated 0 of the 780 non-bonded parameter combinations Excluding 1 bonded neighbours for PPG 7 Excluding 1 bonded neighbours for PPT 14 Excluding 1 bonded neighbours for PDGDG 7 Excluding 1 bonded neighbours for PDGDT 36 Excluding 1 bonded neighbours for PMGDG 50 Excluding 1 bonded neighbours for PMGDT 7 Excluding 1 bonded neighbours for PSQDG 21 Excluding 1 bonded neighbours for PPG 7 Excluding 1 bonded neighbours for PPT 14 Excluding 1 bonded neighbours for PDGDG 7 Excluding 1 bonded neighbours for PDGDT 36 Excluding 1 bonded neighbours for PMGDG 50 Excluding 1 bonded neighbours for PMGDT 7 Excluding 1 bonded neighbours for PSQDG 21 NOTE: System has non-zero total charge: -8.400000e+01 Number of fg atoms 17452 Number of cg atoms 3950 Reading frames from gro file 'GRowing Old MAkes el Chrono Sweat', 3950 atoms. Reading frame 0 time 0.000 Back Off! I just backed up Thylakoide_Membrane_FG_npt2_NoWater_Ions.gro to Thylakoide_Membrane_FG_npt2_NoWater_Ions.gro Water rewrited to normal representation ! ############################### a gro file "Thylakoide_Membrane_FG_npt2_NoWater_Ions.gro" is created with 17452 atom lines, but only the first 3950 lines have coordinates different to 0. Note that the starting conformation of the CG bilayer was constructed with insane.py with the *.itp taken from THYLAKOIDS.zip archive downloaded from the Martini website. With this system I can run CG simulations without problems ? Below the the top files I used : ############ Small_plant_CG_noWater_Ions.top ################ #include "./CG_itp_files/martini_v2.1.itp" #include "./CG_itp_files/martini_v2.0_ions.itp" #include "./CG_itp_files/plantmembrane.itp" [ system ] blabah [ molecules ] ;upperleaflet PPG 7 PPT 14 PDGDG 7 PDGDT 36 PMGDG 50 PMGDT 7 PSQDG 21 ; lower leaflet PPG 7 PPT 14 PDGDG 7 PDGDT 36 PMGDG 50 PMGDT 7 PSQDG 21 ############ Small_plant_FG_noWater_Ions.top ################ #include "./forcefield.ff/forcefield.itp" #include "./FG_itp_files/PPG.itp" #include "./FG_itp_files/PPT.itp" #include "./FG_itp_files/PDGDG.itp" #include "./FG_itp_files/PDGDT.itp" #include "./FG_itp_files/PMGDG.itp" #include "./FG_itp_files/PMGDT.itp" #include "./FG_itp_files/PSQDG.itp" [ system ] [ molecules ] PPG 7 PPT 14 PDGDG 7 PDGDT 36 PMGDG 50 PMGDT 7 PSQDG 21 ; upper leaflet PPG 7 PPT 14 PDGDG 7 PDGT 36 PMGDG 50 PMGDT 7 PSQDG 21 ############################################ Could help me to find where is my error? Stéfane[file "./forcefield.ff/ffG53a6bon.itp", line 576]:
Overriding Proper Dih. parameters,
old: 180 9.35 1 0 0 0
new: OA CH2 CH1 OA 1 0.000 9.50 3
Generated 169 of the 1653 non-bonded parameter combinations
Excluding 3 bonded neighbours for PPG 7
Excluding 3 bonded neighbours for PPT 14
Excluding 3 bonded neighbours for PDGDG 7
Excluding 3 bonded neighbours for PDGDT 36
Excluding 3 bonded neighbours for PMGDG 50
Excluding 3 bonded neighbours for PMGDT 7
Excluding 3 bonded neighbours for PSQDG 21
Excluding 3 bonded neighbours for PPG 7
Excluding 3 bonded neighbours for PPT 14
Excluding 3 bonded neighbours for PDGDG 7
Excluding 3 bonded neighbours for PDGDT 36
Excluding 3 bonded neighbours for PMGDG 50
Excluding 3 bonded neighbours for PMGDT 7
Excluding 3 bonded neighbours for PSQDG 21
NOTE:
System has non-zero total charge: -8.400007e+01
# G96BONDS: 17496
# G96ANGLES: 20326
# PDIHS: 24280
# IDIHS: 2534
# LJ14: 22496
# DIHRES: 1312
calling cpp...
processing topology...
Generated 0 of the 780 non-bonded parameter combinations
Excluding 1 bonded neighbours for PPG 7
Excluding 1 bonded neighbours for PPT 14
Excluding 1 bonded neighbours for PDGDG 7
Excluding 1 bonded neighbours for PDGDT 36
Excluding 1 bonded neighbours for PMGDG 50
Excluding 1 bonded neighbours for PMGDT 7
Excluding 1 bonded neighbours for PSQDG 21
Excluding 1 bonded neighbours for PPG 7
Excluding 1 bonded neighbours for PPT 14
Excluding 1 bonded neighbours for PDGDG 7
Excluding 1 bonded neighbours for PDGDT 36
Excluding 1 bonded neighbours for PMGDG 50
Excluding 1 bonded neighbours for PMGDT 7
Excluding 1 bonded neighbours for PSQDG 21
NOTE:
System has non-zero total charge: -8.400000e+01
Number of fg atoms 17452
Number of cg atoms 3950
Reading frames from gro file 'GRowing Old MAkes el Chrono Sweat', 3950 atoms.
Reading frame 0 time 0.000
Back Off! I just backed up Thylakoide_Membrane_FG_npt2_NoWater_Ions.gro to Thylakoide_Membrane_FG_npt2_NoWater_Ions.gro
Water rewrited to normal representation !
###############################
a gro file "Thylakoide_Membrane_FG_npt2_NoWater_Ions.gro" is created with 17452 atom lines, but only the first 3950 lines have coordinates different to 0. Note that the starting conformation of the CG bilayer was constructed with insane.py with the *.itp taken from THYLAKOIDS.zip archive downloaded from the Martini website. With this system I can run CG simulations without problems ?
Below the the top files I used :
############ Small_plant_CG_noWater_Ions.top ################
#include "./CG_itp_files/martini_v2.1.itp"
#include "./CG_itp_files/martini_v2.0_ions.itp"
#include "./CG_itp_files/plantmembrane.itp"
[ system ]
blabah
[ molecules ]
;upperleaflet
PPG 7
PPT 14
PDGDG 7
PDGDT 36
PMGDG 50
PMGDT 7
PSQDG 21
; lower leaflet
PPG 7
PPT 14
PDGDG 7
PDGDT 36
PMGDG 50
PMGDT 7
PSQDG 21
############ Small_plant_FG_noWater_Ions.top ################
#include "./forcefield.ff/forcefield.itp"
#include "./FG_itp_files/PPG.itp"
#include "./FG_itp_files/PPT.itp"
#include "./FG_itp_files/PDGDG.itp"
#include "./FG_itp_files/PDGDT.itp"
#include "./FG_itp_files/PMGDG.itp"
#include "./FG_itp_files/PMGDT.itp"
#include "./FG_itp_files/PSQDG.itp"
[ system ]
[ molecules ]
PPG 7
PPT 14
PDGDG 7
PDGDT 36
PMGDG 50
PMGDT 7
PSQDG 21
; upper leaflet
PPG 7
PPT 14
PDGDG 7
PDGT 36
PMGDG 50
PMGDT 7
PSQDG 21
############################################
Could help me to find where is my error?
Stéfane
Last edit: 8 years 6 months ago by Stéfane.
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- floris
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8 years 6 months ago #5154
by floris
Replied by floris on topic convertion of a CG membrane to FG one with g_fg2cg
Hi Stefane,
g_fg2cg is in particular sensitive to errors in your input files, unfortunatley it does not always tell you where the error is.
You can ignore the following warning:
WARNING 1 : Overriding Proper Dih. parameters. Use dihedraltype 4 to allow several multiplicity terms. old: 180 9.35 1 180 9.35 1 new: OA CH2 CH1 OA 1 0.000 9.50 3 But what is exactly your problem. I see that Gromacs creates a new gro file (at least it backs the old one up). What happens when you do not specify the -w option ? I never used it myself. A good way to find your error is to try to backmap just one lipid at a time. And please verify if the mapping section in the itp files is not commented (so check if there is a ';'in front of a line, if this is the case, remove them). Good luck Floris[file ffG53a6bon.itp, line 576]:
Overriding Proper Dih. parameters.
Use dihedraltype 4 to allow several multiplicity terms.
old: 180 9.35 1 180 9.35 1
new: OA CH2 CH1 OA 1 0.000 9.50 3
But what is exactly your problem. I see that Gromacs creates a new gro file (at least it backs the old one up).
What happens when you do not specify the -w option ? I never used it myself.
A good way to find your error is to try to backmap just one lipid at a time.
And please verify if the mapping section in the itp files is not commented (so check if there is a ';'in front of a line, if this is the case, remove them).
Good luck
Floris
g_fg2cg is in particular sensitive to errors in your input files, unfortunatley it does not always tell you where the error is.
You can ignore the following warning:
WARNING 1 : Overriding Proper Dih. parameters. Use dihedraltype 4 to allow several multiplicity terms. old: 180 9.35 1 180 9.35 1 new: OA CH2 CH1 OA 1 0.000 9.50 3 But what is exactly your problem. I see that Gromacs creates a new gro file (at least it backs the old one up). What happens when you do not specify the -w option ? I never used it myself. A good way to find your error is to try to backmap just one lipid at a time. And please verify if the mapping section in the itp files is not commented (so check if there is a ';'in front of a line, if this is the case, remove them). Good luck Floris[file ffG53a6bon.itp, line 576]:
Overriding Proper Dih. parameters.
Use dihedraltype 4 to allow several multiplicity terms.
old: 180 9.35 1 180 9.35 1
new: OA CH2 CH1 OA 1 0.000 9.50 3
But what is exactly your problem. I see that Gromacs creates a new gro file (at least it backs the old one up).
What happens when you do not specify the -w option ? I never used it myself.
A good way to find your error is to try to backmap just one lipid at a time.
And please verify if the mapping section in the itp files is not commented (so check if there is a ';'in front of a line, if this is the case, remove them).
Good luck
Floris
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- Stéfane
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8 years 6 months ago #5165
by Stéfane
Replied by Stéfane on topic convertion of a CG membrane to FG one with g_fg2cg
Thank you Floris for you message. You are right, a gro file is created with the correct FG residue and atom names for my CG lipids but my problem is taht only the first 3950 atoms have coordinates different of 0 (see below).
###################
.....
61S1AL C108 3943 6.044 7.709 4.652
61S1AL C109 3944 5.962 7.731 5.000
61S1AL C110 3945 5.854 7.998 5.224
61S1AL C111 3946 5.943 7.724 5.575
61S1AL C112 3947 5.548 7.895 4.670
61S1AL C113 3948 5.476 7.791 5.010
61S1AL C114 3949 5.289 8.109 5.202
61S1AL C115 3950 5.422 7.892 5.580
61S1AL C116 3951 0.000 0.000 0.000 ***
61S1AL C117 3952 0.000 0.000 0.000
61S1AL C118 3953 0.000 0.000 0.000
61S1AL CGS2 3954 0.000 0.000 0.000
61S1AL OGS2 3955 0.000 0.000 0.000
61S1AL CES2 3956 0.000 0.000 0.000
61S1AL OES2 3957 0.000 0.000 0.000
61S1AL C202 3958 0.000 0.000 0.000
61S1AL C203 3959 0.000 0.000 0.000
61S1AL C204 3960 0.000 0.000 0.000
61S1AL C205 3961 0.000 0.000 0.000
61S1AL C206 3962 0.000 0.000 0.000
61S1AL C207 3963 0.000 0.000 0.000
61S1AL C208 3964 0.000 0.000 0.000
61S1AL C209 3965 0.000 0.000 0.000
61S1AL C210 3966 0.000 0.000 0.000
....
#########
If I don't use the -wat flag, the program crashes :
calling cpp...
In file included from ./forcefield.ff/forcefield.itp:8,
from Small_plant_FG_noWater_Ions.top:1:
./forcefield.ff/ffG53a6nb.itp:246:55: warning: missing terminating ' character
./forcefield.ff/ffG53a6nb.itp:257:57: warning: missing terminating ' character
processing topology...
WARNING 1 : Overriding Proper Dih. parameters, old: 180 9.35 1 0 0 0 new: OA CH2 CH1 OA 1 0.000 9.50 3 Generated 169 of the 1653 non-bonded parameter combinations Excluding 3 bonded neighbours for PPG 7 Excluding 3 bonded neighbours for PPT 14 Excluding 3 bonded neighbours for PDGDG 7 Excluding 3 bonded neighbours for PDGDT 36 Excluding 3 bonded neighbours for PMGDG 50 Excluding 3 bonded neighbours for PMGDT 7 Excluding 3 bonded neighbours for PSQDG 21 Excluding 3 bonded neighbours for PPG 7 Excluding 3 bonded neighbours for PPT 14 Excluding 3 bonded neighbours for PDGDG 7 Excluding 3 bonded neighbours for PDGDT 36 Excluding 3 bonded neighbours for PMGDG 50 Excluding 3 bonded neighbours for PMGDT 7 Excluding 3 bonded neighbours for PSQDG 21 NOTE: System has non-zero total charge: -8.400007e+01 # G96BONDS: 17496 # G96ANGLES: 20326 # PDIHS: 24280 # IDIHS: 2534 # LJ14: 22496 # DIHRES: 1312 calling cpp... processing topology... Generated 0 of the 780 non-bonded parameter combinations Excluding 1 bonded neighbours for PPG 7 Excluding 1 bonded neighbours for PPT 14 Excluding 1 bonded neighbours for PDGDG 7 Excluding 1 bonded neighbours for PDGDT 36 Excluding 1 bonded neighbours for PMGDG 50 Excluding 1 bonded neighbours for PMGDT 7 Excluding 1 bonded neighbours for PSQDG 21 Excluding 1 bonded neighbours for PPG 7 Excluding 1 bonded neighbours for PPT 14 Excluding 1 bonded neighbours for PDGDG 7 Excluding 1 bonded neighbours for PDGDT 36 Excluding 1 bonded neighbours for PMGDG 50 Excluding 1 bonded neighbours for PMGDT 7 Excluding 1 bonded neighbours for PSQDG 21 NOTE: System has non-zero total charge: -8.400000e+01 Number of fg atoms 17452 Number of cg atoms 3950 Reading frames from gro file 'GRowing Old MAkes el Chrono Sweat', 3950 atoms. Reading frame 0 time 0.000 1445528781 Name of CG water in topology should be W Segmentation fault (core dumped) Stéfane[file "./forcefield.ff/ffG53a6bon.itp", line 576]:
Overriding Proper Dih. parameters,
old: 180 9.35 1 0 0 0
new: OA CH2 CH1 OA 1 0.000 9.50 3
Generated 169 of the 1653 non-bonded parameter combinations
Excluding 3 bonded neighbours for PPG 7
Excluding 3 bonded neighbours for PPT 14
Excluding 3 bonded neighbours for PDGDG 7
Excluding 3 bonded neighbours for PDGDT 36
Excluding 3 bonded neighbours for PMGDG 50
Excluding 3 bonded neighbours for PMGDT 7
Excluding 3 bonded neighbours for PSQDG 21
Excluding 3 bonded neighbours for PPG 7
Excluding 3 bonded neighbours for PPT 14
Excluding 3 bonded neighbours for PDGDG 7
Excluding 3 bonded neighbours for PDGDT 36
Excluding 3 bonded neighbours for PMGDG 50
Excluding 3 bonded neighbours for PMGDT 7
Excluding 3 bonded neighbours for PSQDG 21
NOTE:
System has non-zero total charge: -8.400007e+01
# G96BONDS: 17496
# G96ANGLES: 20326
# PDIHS: 24280
# IDIHS: 2534
# LJ14: 22496
# DIHRES: 1312
calling cpp...
processing topology...
Generated 0 of the 780 non-bonded parameter combinations
Excluding 1 bonded neighbours for PPG 7
Excluding 1 bonded neighbours for PPT 14
Excluding 1 bonded neighbours for PDGDG 7
Excluding 1 bonded neighbours for PDGDT 36
Excluding 1 bonded neighbours for PMGDG 50
Excluding 1 bonded neighbours for PMGDT 7
Excluding 1 bonded neighbours for PSQDG 21
Excluding 1 bonded neighbours for PPG 7
Excluding 1 bonded neighbours for PPT 14
Excluding 1 bonded neighbours for PDGDG 7
Excluding 1 bonded neighbours for PDGDT 36
Excluding 1 bonded neighbours for PMGDG 50
Excluding 1 bonded neighbours for PMGDT 7
Excluding 1 bonded neighbours for PSQDG 21
NOTE:
System has non-zero total charge: -8.400000e+01
Number of fg atoms 17452
Number of cg atoms 3950
Reading frames from gro file 'GRowing Old MAkes el Chrono Sweat', 3950 atoms.
Reading frame 0 time 0.000 1445528781
Name of CG water in topology should be W
Segmentation fault (core dumped)
Stéfane
###################
.....
61S1AL C108 3943 6.044 7.709 4.652
61S1AL C109 3944 5.962 7.731 5.000
61S1AL C110 3945 5.854 7.998 5.224
61S1AL C111 3946 5.943 7.724 5.575
61S1AL C112 3947 5.548 7.895 4.670
61S1AL C113 3948 5.476 7.791 5.010
61S1AL C114 3949 5.289 8.109 5.202
61S1AL C115 3950 5.422 7.892 5.580
61S1AL C116 3951 0.000 0.000 0.000 ***
61S1AL C117 3952 0.000 0.000 0.000
61S1AL C118 3953 0.000 0.000 0.000
61S1AL CGS2 3954 0.000 0.000 0.000
61S1AL OGS2 3955 0.000 0.000 0.000
61S1AL CES2 3956 0.000 0.000 0.000
61S1AL OES2 3957 0.000 0.000 0.000
61S1AL C202 3958 0.000 0.000 0.000
61S1AL C203 3959 0.000 0.000 0.000
61S1AL C204 3960 0.000 0.000 0.000
61S1AL C205 3961 0.000 0.000 0.000
61S1AL C206 3962 0.000 0.000 0.000
61S1AL C207 3963 0.000 0.000 0.000
61S1AL C208 3964 0.000 0.000 0.000
61S1AL C209 3965 0.000 0.000 0.000
61S1AL C210 3966 0.000 0.000 0.000
....
#########
If I don't use the -wat flag, the program crashes :
calling cpp...
In file included from ./forcefield.ff/forcefield.itp:8,
from Small_plant_FG_noWater_Ions.top:1:
./forcefield.ff/ffG53a6nb.itp:246:55: warning: missing terminating ' character
./forcefield.ff/ffG53a6nb.itp:257:57: warning: missing terminating ' character
processing topology...
WARNING 1 : Overriding Proper Dih. parameters, old: 180 9.35 1 0 0 0 new: OA CH2 CH1 OA 1 0.000 9.50 3 Generated 169 of the 1653 non-bonded parameter combinations Excluding 3 bonded neighbours for PPG 7 Excluding 3 bonded neighbours for PPT 14 Excluding 3 bonded neighbours for PDGDG 7 Excluding 3 bonded neighbours for PDGDT 36 Excluding 3 bonded neighbours for PMGDG 50 Excluding 3 bonded neighbours for PMGDT 7 Excluding 3 bonded neighbours for PSQDG 21 Excluding 3 bonded neighbours for PPG 7 Excluding 3 bonded neighbours for PPT 14 Excluding 3 bonded neighbours for PDGDG 7 Excluding 3 bonded neighbours for PDGDT 36 Excluding 3 bonded neighbours for PMGDG 50 Excluding 3 bonded neighbours for PMGDT 7 Excluding 3 bonded neighbours for PSQDG 21 NOTE: System has non-zero total charge: -8.400007e+01 # G96BONDS: 17496 # G96ANGLES: 20326 # PDIHS: 24280 # IDIHS: 2534 # LJ14: 22496 # DIHRES: 1312 calling cpp... processing topology... Generated 0 of the 780 non-bonded parameter combinations Excluding 1 bonded neighbours for PPG 7 Excluding 1 bonded neighbours for PPT 14 Excluding 1 bonded neighbours for PDGDG 7 Excluding 1 bonded neighbours for PDGDT 36 Excluding 1 bonded neighbours for PMGDG 50 Excluding 1 bonded neighbours for PMGDT 7 Excluding 1 bonded neighbours for PSQDG 21 Excluding 1 bonded neighbours for PPG 7 Excluding 1 bonded neighbours for PPT 14 Excluding 1 bonded neighbours for PDGDG 7 Excluding 1 bonded neighbours for PDGDT 36 Excluding 1 bonded neighbours for PMGDG 50 Excluding 1 bonded neighbours for PMGDT 7 Excluding 1 bonded neighbours for PSQDG 21 NOTE: System has non-zero total charge: -8.400000e+01 Number of fg atoms 17452 Number of cg atoms 3950 Reading frames from gro file 'GRowing Old MAkes el Chrono Sweat', 3950 atoms. Reading frame 0 time 0.000 1445528781 Name of CG water in topology should be W Segmentation fault (core dumped) Stéfane[file "./forcefield.ff/ffG53a6bon.itp", line 576]:
Overriding Proper Dih. parameters,
old: 180 9.35 1 0 0 0
new: OA CH2 CH1 OA 1 0.000 9.50 3
Generated 169 of the 1653 non-bonded parameter combinations
Excluding 3 bonded neighbours for PPG 7
Excluding 3 bonded neighbours for PPT 14
Excluding 3 bonded neighbours for PDGDG 7
Excluding 3 bonded neighbours for PDGDT 36
Excluding 3 bonded neighbours for PMGDG 50
Excluding 3 bonded neighbours for PMGDT 7
Excluding 3 bonded neighbours for PSQDG 21
Excluding 3 bonded neighbours for PPG 7
Excluding 3 bonded neighbours for PPT 14
Excluding 3 bonded neighbours for PDGDG 7
Excluding 3 bonded neighbours for PDGDT 36
Excluding 3 bonded neighbours for PMGDG 50
Excluding 3 bonded neighbours for PMGDT 7
Excluding 3 bonded neighbours for PSQDG 21
NOTE:
System has non-zero total charge: -8.400007e+01
# G96BONDS: 17496
# G96ANGLES: 20326
# PDIHS: 24280
# IDIHS: 2534
# LJ14: 22496
# DIHRES: 1312
calling cpp...
processing topology...
Generated 0 of the 780 non-bonded parameter combinations
Excluding 1 bonded neighbours for PPG 7
Excluding 1 bonded neighbours for PPT 14
Excluding 1 bonded neighbours for PDGDG 7
Excluding 1 bonded neighbours for PDGDT 36
Excluding 1 bonded neighbours for PMGDG 50
Excluding 1 bonded neighbours for PMGDT 7
Excluding 1 bonded neighbours for PSQDG 21
Excluding 1 bonded neighbours for PPG 7
Excluding 1 bonded neighbours for PPT 14
Excluding 1 bonded neighbours for PDGDG 7
Excluding 1 bonded neighbours for PDGDT 36
Excluding 1 bonded neighbours for PMGDG 50
Excluding 1 bonded neighbours for PMGDT 7
Excluding 1 bonded neighbours for PSQDG 21
NOTE:
System has non-zero total charge: -8.400000e+01
Number of fg atoms 17452
Number of cg atoms 3950
Reading frames from gro file 'GRowing Old MAkes el Chrono Sweat', 3950 atoms.
Reading frame 0 time 0.000 1445528781
Name of CG water in topology should be W
Segmentation fault (core dumped)
Stéfane
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- floris
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8 years 5 months ago #5167
by floris
Replied by floris on topic convertion of a CG membrane to FG one with g_fg2cg
Hmmm, this seems as a though problem,
I have never used the -wat flag, so I am suprised you have to use it (it might be that your have a different version).
What happens if you would only try to convert the atoms starting at 3951?
I have never used the -wat flag, so I am suprised you have to use it (it might be that your have a different version).
What happens if you would only try to convert the atoms starting at 3951?
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- Stéfane
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8 years 5 months ago - 8 years 5 months ago #5168
by Stéfane
Replied by Stéfane on topic convertion of a CG membrane to FG one with g_fg2cg
Floris,
>> What happens if you would only try to convert the atoms starting at 3951?
Could be more specific? Do you want ttaht I convert my CG system into FG one ? My CG gro file contains only the lipids with 3950 particles. This is why what is the problem.
Stefane
>> What happens if you would only try to convert the atoms starting at 3951?
Could be more specific? Do you want ttaht I convert my CG system into FG one ? My CG gro file contains only the lipids with 3950 particles. This is why what is the problem.
Stefane
Last edit: 8 years 5 months ago by Stéfane.
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8 years 5 months ago #5169
by floris
Replied by floris on topic convertion of a CG membrane to FG one with g_fg2cg
It is indeed a strange problem. So your FG gro file only has coordinates for the amount of particles that your CG gro file contains?
Try to set your -wat setting to 0. There might be a bug related to that.
Because you do not have any water right?
Try to set your -wat setting to 0. There might be a bug related to that.
Because you do not have any water right?
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8 years 5 months ago #5170
by mnmelo
Replied by mnmelo on topic convertion of a CG membrane to FG one with g_fg2cg
A newer/faster/cleaner alternative to the cumbersome g_fg2cg is the
Backward
method.
Maybe its worth it giving it a try?
Maybe its worth it giving it a try?
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8 years 5 months ago #5171
by floris
Replied by floris on topic convertion of a CG membrane to FG one with g_fg2cg
Backward is indeed much nicer to work with.
You will only have to create the mappings though, which should not be a problem for SQDG and MGDG, but for DGDG it will not be easy....
You will only have to create the mappings though, which should not be a problem for SQDG and MGDG, but for DGDG it will not be easy....
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8 years 5 months ago #5172
by Stéfane
Replied by Stéfane on topic convertion of a CG membrane to FG one with g_fg2cg
@Floris, I will test the g_fg2cG comamnd with the wat flag set to 1.
@nmelo, I am also testing the backward approach, since I would like to simulate a protein bounded to a model of thylakoid membrane with the CHARMM36 force field. if I have some questions, I will create another topic
Stéfane
@nmelo, I am also testing the backward approach, since I would like to simulate a protein bounded to a model of thylakoid membrane with the CHARMM36 force field. if I have some questions, I will create another topic
Stéfane
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