martini wrote: Désolée encore moi.
IL n'y a pas une étape qui se fait sans qu'un problème intervient.
Voilà j'ai réussi à lancer une minimisation sur mon système. Jusque la tout c'est bien dérouler. Du coup j'ai voulu lancer une vrai simulation et une seule frame en sort :o

J'ai utilisé le fichier mdp suivant ( fournit pas le site ) :

;
; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0 or 2.1
;

; TIMESTEP IN MARTINI
; Most simulations are numerically stable
; with dt=40 fs, some (especially rings) require 20-30 fs.
; Note that time steps of 40 fs and larger may create local heating or
; cooling in your system. Although the use of a heat bath will globally
; remove this effect, it is advised to check consistency of
; your results for somewhat smaller time steps in the range 20-30 fs.
; Time steps exceeding 40 fs should not be used; time steps smaller
; than 20 fs are also not required.

integrator = md
tinit = 0.0
dt = 0.02
nsteps = 500000
nstcomm = 1
comm-grps =

nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstenergy = 100
nstxtcout = 1000
xtc_precision = 100
xtc-grps =
energygrps = Protein

; NEIGHBOURLIST and MARTINI
; Due to the use of shifted potentials, the noise generated
; from particles leaving/entering the neighbour list is not so large,
; even when large time steps are being used. In practice, once every
; ten steps works fine with a neighborlist cutoff that is equal to the
; non-bonded cutoff (1.2 nm). However, to improve energy conservation
; or to avoid local heating/cooling, you may increase the update frequency
; and/or enlarge the neighbourlist cut-off (to 1.4 nm). The latter option
; is computationally less expensive and leads to improved energy conservation

nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4

; MARTINI and NONBONDED
; Standard cut-off schemes are used for the non-bonded interactions
; in the Martini model: LJ interactions are shifted to zero in the
; range 0.9-1.2 nm, and electrostatic interactions in the range 0.0-1.2 nm.
; The treatment of the non-bonded cut-offs is considered to be part of
; the force field parameterization, so we recommend not to touch these
; values as they will alter the overall balance of the force field.
; In principle you can include long range electrostatics through the use
; of PME, which could be more realistic in certain applications
; Please realize that electrostatic interactions in the Martini model are
; not considered to be very accurate to begin with, especially as the
; screening in the system is set to be uniform across the system with
; a screening constant of 15. When using PME, please make sure your
; system properties are still reasonable.

coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No

; MARTINI and TEMPRATURE/PRESSURE
; normal temperature and pressure coupling schemes can be used.
; It is recommended to couple individual groups in your system separately.
; Good temperature control can be achieved with the Berendsen thermostat,
; using a coupling constant of the order of Ï„ = 1 ps. Even better
; temperature control can be achieved by reducing the temperature coupling
; constant to 0.1 ps, although with such tight coupling (Ï„ approaching
; the time step) one can no longer speak of a weak-coupling scheme.
; We therefore recommend a coupling time constant of at least 0.5 ps.
;
; Similarly, pressure can be controlled with the Berendsen barostat,
; with a coupling constant in the range 1-5 ps and typical compressibility
; in the order of 10-4 - 10-5 bar-1. Note that, in order to estimate
; compressibilities from CG simulations, you should use Parrinello-Rahman
; type coupling.

tcoupl = Berendsen
tc-grps = system
tau_t = 1.0
ref_t = 320
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 1.0
compressibility = 3e-4
ref_p = 1.0

gen_vel = no
gen_temp = 320
gen_seed = 473529

; MARTINI and CONSTRAINTS
; for ring systems constraints are defined
; which are best handled using Lincs.
; Note, during energy minimization the constrainst should be
; replaced by stiff bonds.

constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30

Lors de la création du fichier tpr avec le grompp de warning sont sortit :

"NOTE 1 : nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file md.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. WARNING 1 [file md.mdp]: For proper integration of the Berendsen barostat, tau_p (1) should be at least 10 times larger than nstpcouple*dt (0.2) Generated 0 of the 780 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Protein_A' Excluding 1 bonded neighbours molecule type 'W' NOTE 3 [file system.top, line 14]: System has non-zero total charge: 6.000000 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. WARNING 2 [file system.top, line 14]: The bond in molecule-type Protein_A between atoms 1 BB and 2 BB has an estimated oscillational period of 9.7e-02 ps, which is less than 5 times the time step of 2.0e-02 ps. Maybe you forgot to change the constraints mdp option. " Du coup je me suis permis de les ignorer avec Maxwarn. Mais une fois le run lancé il ne dure moins de 5 min sur 16 processor :o TU aurais une idée de ce qui se passe??? Encore désolée avec toutes mes questions.[/quote][file md.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy


NOTE 2 : The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. WARNING 1 [file md.mdp]: For proper integration of the Berendsen barostat, tau_p (1) should be at least 10 times larger than nstpcouple*dt (0.2) Generated 0 of the 780 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Protein_A' Excluding 1 bonded neighbours molecule type 'W' NOTE 3 [file system.top, line 14]: System has non-zero total charge: 6.000000 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. WARNING 2 [file system.top, line 14]: The bond in molecule-type Protein_A between atoms 1 BB and 2 BB has an estimated oscillational period of 9.7e-02 ps, which is less than 5 times the time step of 2.0e-02 ps. Maybe you forgot to change the constraints mdp option. " Du coup je me suis permis de les ignorer avec Maxwarn. Mais une fois le run lancé il ne dure moins de 5 min sur 16 processor :o TU aurais une idée de ce qui se passe??? Encore désolée avec toutes mes questions.[/quote][file md.mdp]:
The Berendsen thermostat does not generate the correct kinetic energy
distribution. You might want to consider using the V-rescale thermostat.


WARNING 1 : For proper integration of the Berendsen barostat, tau_p (1) should be at least 10 times larger than nstpcouple*dt (0.2) Generated 0 of the 780 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Protein_A' Excluding 1 bonded neighbours molecule type 'W' NOTE 3 [file system.top, line 14]: System has non-zero total charge: 6.000000 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. WARNING 2 [file system.top, line 14]: The bond in molecule-type Protein_A between atoms 1 BB and 2 BB has an estimated oscillational period of 9.7e-02 ps, which is less than 5 times the time step of 2.0e-02 ps. Maybe you forgot to change the constraints mdp option. " Du coup je me suis permis de les ignorer avec Maxwarn. Mais une fois le run lancé il ne dure moins de 5 min sur 16 processor :o TU aurais une idée de ce qui se passe??? Encore désolée avec toutes mes questions.[/quote][file md.mdp]:
For proper integration of the Berendsen barostat, tau_p (1) should be at
least 10 times larger than nstpcouple*dt (0.2)

Generated 0 of the 780 non-bonded parameter combinations
Excluding 1 bonded neighbours molecule type 'Protein_A'
Excluding 1 bonded neighbours molecule type 'W'

NOTE 3 : System has non-zero total charge: 6.000000 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. WARNING 2 [file system.top, line 14]: The bond in molecule-type Protein_A between atoms 1 BB and 2 BB has an estimated oscillational period of 9.7e-02 ps, which is less than 5 times the time step of 2.0e-02 ps. Maybe you forgot to change the constraints mdp option. " Du coup je me suis permis de les ignorer avec Maxwarn. Mais une fois le run lancé il ne dure moins de 5 min sur 16 processor :o TU aurais une idée de ce qui se passe??? Encore désolée avec toutes mes questions.[/quote][file system.top, line 14]:
System has non-zero total charge: 6.000000
Total charge should normally be an integer. See
www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.




WARNING 2 : The bond in molecule-type Protein_A between atoms 1 BB and 2 BB has an estimated oscillational period of 9.7e-02 ps, which is less than 5 times the time step of 2.0e-02 ps. Maybe you forgot to change the constraints mdp option. " Du coup je me suis permis de les ignorer avec Maxwarn. Mais une fois le run lancé il ne dure moins de 5 min sur 16 processor :o TU aurais une idée de ce qui se passe??? Encore désolée avec toutes mes questions.[/quote][file system.top, line 14]:
The bond in molecule-type Protein_A between atoms 1 BB and 2 BB has an
estimated oscillational period of 9.7e-02 ps, which is less than 5 times
the time step of 2.0e-02 ps.
Maybe you forgot to change the constraints mdp option.

"

Du coup je me suis permis de les ignorer avec Maxwarn.
Mais une fois le run lancé il ne dure moins de 5 min sur 16 processor :o

TU aurais une idée de ce qui se passe???

Encore désolée avec toutes mes questions.

martini wrote: Yes you are right sorry for the french :p

I change my mdp file like this:

; It is recommended to couple individual groups in your system separately.
; Good temperature control can be achieved with the Berendsen thermostat,
; using a coupling constant of the order of Ï„ = 1 ps. Even better
; temperature control can be achieved by reducing the temperature coupling
; constant to 0.1 ps, although with such tight coupling (Ï„ approaching
; the time step) one can no longer speak of a weak-coupling scheme.
; We therefore recommend a coupling time constant of at least 0.5 ps.
;
; Similarly, pressure can be controlled with the Berendsen barostat,
; with a coupling constant in the range 1-5 ps and typical compressibility
; in the order of 10-4 - 10-5 bar-1. Note that, in order to estimate
; compressibilities from CG simulations, you should use Parrinello-Rahman
; type coupling.

tcoupl = v-rescale[size=?][/size]
tc-grps = system
tau_t = 1.0
ref_t = 320
Pcoupl = berendsen
Pcoupltype = isotropic
[size=?]tau_p = 2.0[/size]
compressibility = 3e-4
ref_p = 1.0

gen_vel = no
gen_temp = 320
gen_seed = 473529

; MARTINI and CONSTRAINTS
; for ring systems constraints are defined
; which are best handled using Lincs.
; Note, during energy minimization the constrainst should be
; replaced by stiff bonds.

constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4


Now I have just one warning:

"NOTE 1 : nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy Generated 0 of the 780 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Protein_A' Excluding 1 bonded neighbours molecule type 'W' NOTE 2 [file system.top, line 14]: System has non-zero total charge: 6.000000 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. WARNING 1 [file system.top, line 14]: The bond in molecule-type Protein_A between atoms 1 BB and 2 BB has an estimated oscillational period of 9.7e-02 ps, which is less than 5 times the time step of 2.0e-02 ps. Maybe you forgot to change the constraints mdp option." ANd my system does not want to go more than one frame :( I don't really understant the warning about constraint. I hope I don't disturb you to much. Thank you very very much for your help[/quote][file md.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy

Generated 0 of the 780 non-bonded parameter combinations
Excluding 1 bonded neighbours molecule type 'Protein_A'
Excluding 1 bonded neighbours molecule type 'W'

NOTE 2 : System has non-zero total charge: 6.000000 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. WARNING 1 [file system.top, line 14]: The bond in molecule-type Protein_A between atoms 1 BB and 2 BB has an estimated oscillational period of 9.7e-02 ps, which is less than 5 times the time step of 2.0e-02 ps. Maybe you forgot to change the constraints mdp option." ANd my system does not want to go more than one frame :( I don't really understant the warning about constraint. I hope I don't disturb you to much. Thank you very very much for your help[/quote][file system.top, line 14]:
System has non-zero total charge: 6.000000
Total charge should normally be an integer. See
www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.


WARNING 1 : The bond in molecule-type Protein_A between atoms 1 BB and 2 BB has an estimated oscillational period of 9.7e-02 ps, which is less than 5 times the time step of 2.0e-02 ps. Maybe you forgot to change the constraints mdp option." ANd my system does not want to go more than one frame :( I don't really understant the warning about constraint. I hope I don't disturb you to much. Thank you very very much for your help[/quote][file system.top, line 14]:
The bond in molecule-type Protein_A between atoms 1 BB and 2 BB has an
estimated oscillational period of 9.7e-02 ps, which is less than 5 times
the time step of 2.0e-02 ps.
Maybe you forgot to change the constraints mdp option."


ANd my system does not want to go more than one frame :(

I don't really understant the warning about constraint.

I hope I don't disturb you to much.

Thank you very very much for your help

martini wrote: :o

the system seems not crash :)

martini wrote: Hi Xavier,

My simulation worked well ;)

Thanks a lot for your help.

Now I try to compute a reverse transformation to my last frame of coarse grained simulation in all atom "file" but when I use this command:

g_fg2cg -pfg topol.top -pcg system.top -n 0 -c cg.gro -o all_atm.gro

I obtain this error:
System has non-zero total charge: 6.000000e+00


Number of fg atoms 108324
Number of cg atoms 9209
Reading frames from gro file 'Generated by trjconv : Martini system from x.pdb t= 5000.00000', 9209 atoms.
Reading frame 0 time 5000.000 1368774392
Name of CG water in topology should be W
Erreur de segmentation (core dumped)

Did you see this kind of error before??

Its strange because Its not the first time that I compute a reverse transformation and I never had error and now I obtain this one and I don't know what does it mean?
For me "segmentation fault" its when you don't have enought place but why there is a problem with water name while in the topology file from "cg" there is "w" for water resname :o

If you have any sugestion I take it

Thanks a lot

thu nguyen wrote: Hi martini,

Maybe the fg.top file should include fg_w.itp (FG water topology). And the fg water name should changed to FG_W. And you can check forcefield included in .top file.

I just have met this error. I followed theses step, and it worked :-)

Thu