anirbanzz wrote: Hi,

I have simulated a CG system containing multiple copies of a protein in a DSPC bilayer with water using MARTINI FF. Now I am trying to convert this CG model to all-atom FG model using the modified gromacs_reverse code command g_fg2cg. Bu I am getting the Segmentation Fault message as:

Excluding 1 bonded neighbours for Protein 1
Excluding 1 bonded neighbours for DSPC 104
Excluding 1 bonded neighbours for W 1397
Excluding 1 bonded neighbours for NA+ 0
Excluding 1 bonded neighbours for CL- 4

Number of fg atoms 410288
Number of cg atoms 57296
Reading frames from gro file 'B2AR in DSPC Bilayer', 57296 atoms.
Reading frame 0 time 0.000 1297343418
Segmentation fault


How to solve this? Please suggest.


Thanks,

Anirban

anirbanzz wrote: Thanks XAvier for the reply. Yes, the problem happened because of DSPC mapping issue. Now, I am just trying to convert back the protein molecules only and I have been successful in that. Bu, now when I try to run SA, grompp is throwing error as:


creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
WARNING 1 : Unknown left-hand 'cap_force' in parameter file WARNING 2 [file fg_protein.mdp, line unknown]: Unknown left-hand 'cap_a' in parameter file WARNING 3 [file fg_protein.mdp, line unknown]: Unknown left-hand 'fc_restr' in parameter file WARNING 4 [file fg_protein.mdp, line unknown]: Unknown left-hand 'r_CGW' in parameter file WARNING 5 [file fg_protein.mdp, line unknown]: Unknown left-hand 'fc_restrW' in parameter file WARNING 6 [file fg_protein.mdp, line unknown]: Unknown left-hand 'rel_steps' in parameter file WARNING 7 [file fg_protein.mdp, line unknown]: Unknown left-hand 'rel_water' in parameter file checking input for internal consistency... calling /lib/cpp... --------------------------------------------------------------------------------- My system contains only multiple copies of a protein. So in what way should I chage the .mdp file that is given in the "reverse tutorial"? And if I continue with these warnings, then SA MD shows parts of the proteins falling apart. Please suggest. Thanks, Anirban[/quote] You probably use an mdp file that is for a more recent version of GMX. Did you try to use the one given in the tutorial and adapt it to your system?[file fg_protein.mdp, line unknown]:
Unknown left-hand 'cap_force' in parameter file

WARNING 2 : Unknown left-hand 'cap_a' in parameter file WARNING 3 [file fg_protein.mdp, line unknown]: Unknown left-hand 'fc_restr' in parameter file WARNING 4 [file fg_protein.mdp, line unknown]: Unknown left-hand 'r_CGW' in parameter file WARNING 5 [file fg_protein.mdp, line unknown]: Unknown left-hand 'fc_restrW' in parameter file WARNING 6 [file fg_protein.mdp, line unknown]: Unknown left-hand 'rel_steps' in parameter file WARNING 7 [file fg_protein.mdp, line unknown]: Unknown left-hand 'rel_water' in parameter file checking input for internal consistency... calling /lib/cpp... --------------------------------------------------------------------------------- My system contains only multiple copies of a protein. So in what way should I chage the .mdp file that is given in the "reverse tutorial"? And if I continue with these warnings, then SA MD shows parts of the proteins falling apart. Please suggest. Thanks, Anirban[/quote] You probably use an mdp file that is for a more recent version of GMX. Did you try to use the one given in the tutorial and adapt it to your system?[file fg_protein.mdp, line unknown]:
Unknown left-hand 'cap_a' in parameter file

WARNING 3 : Unknown left-hand 'fc_restr' in parameter file WARNING 4 [file fg_protein.mdp, line unknown]: Unknown left-hand 'r_CGW' in parameter file WARNING 5 [file fg_protein.mdp, line unknown]: Unknown left-hand 'fc_restrW' in parameter file WARNING 6 [file fg_protein.mdp, line unknown]: Unknown left-hand 'rel_steps' in parameter file WARNING 7 [file fg_protein.mdp, line unknown]: Unknown left-hand 'rel_water' in parameter file checking input for internal consistency... calling /lib/cpp... --------------------------------------------------------------------------------- My system contains only multiple copies of a protein. So in what way should I chage the .mdp file that is given in the "reverse tutorial"? And if I continue with these warnings, then SA MD shows parts of the proteins falling apart. Please suggest. Thanks, Anirban[/quote] You probably use an mdp file that is for a more recent version of GMX. Did you try to use the one given in the tutorial and adapt it to your system?[file fg_protein.mdp, line unknown]:
Unknown left-hand 'fc_restr' in parameter file

WARNING 4 : Unknown left-hand 'r_CGW' in parameter file WARNING 5 [file fg_protein.mdp, line unknown]: Unknown left-hand 'fc_restrW' in parameter file WARNING 6 [file fg_protein.mdp, line unknown]: Unknown left-hand 'rel_steps' in parameter file WARNING 7 [file fg_protein.mdp, line unknown]: Unknown left-hand 'rel_water' in parameter file checking input for internal consistency... calling /lib/cpp... --------------------------------------------------------------------------------- My system contains only multiple copies of a protein. So in what way should I chage the .mdp file that is given in the "reverse tutorial"? And if I continue with these warnings, then SA MD shows parts of the proteins falling apart. Please suggest. Thanks, Anirban[/quote] You probably use an mdp file that is for a more recent version of GMX. Did you try to use the one given in the tutorial and adapt it to your system?[file fg_protein.mdp, line unknown]:
Unknown left-hand 'r_CGW' in parameter file

WARNING 5 : Unknown left-hand 'fc_restrW' in parameter file WARNING 6 [file fg_protein.mdp, line unknown]: Unknown left-hand 'rel_steps' in parameter file WARNING 7 [file fg_protein.mdp, line unknown]: Unknown left-hand 'rel_water' in parameter file checking input for internal consistency... calling /lib/cpp... --------------------------------------------------------------------------------- My system contains only multiple copies of a protein. So in what way should I chage the .mdp file that is given in the "reverse tutorial"? And if I continue with these warnings, then SA MD shows parts of the proteins falling apart. Please suggest. Thanks, Anirban[/quote] You probably use an mdp file that is for a more recent version of GMX. Did you try to use the one given in the tutorial and adapt it to your system?[file fg_protein.mdp, line unknown]:
Unknown left-hand 'fc_restrW' in parameter file

WARNING 6 : Unknown left-hand 'rel_steps' in parameter file WARNING 7 [file fg_protein.mdp, line unknown]: Unknown left-hand 'rel_water' in parameter file checking input for internal consistency... calling /lib/cpp... --------------------------------------------------------------------------------- My system contains only multiple copies of a protein. So in what way should I chage the .mdp file that is given in the "reverse tutorial"? And if I continue with these warnings, then SA MD shows parts of the proteins falling apart. Please suggest. Thanks, Anirban[/quote] You probably use an mdp file that is for a more recent version of GMX. Did you try to use the one given in the tutorial and adapt it to your system?[file fg_protein.mdp, line unknown]:
Unknown left-hand 'rel_steps' in parameter file

WARNING 7 : Unknown left-hand 'rel_water' in parameter file checking input for internal consistency... calling /lib/cpp... --------------------------------------------------------------------------------- My system contains only multiple copies of a protein. So in what way should I chage the .mdp file that is given in the "reverse tutorial"? And if I continue with these warnings, then SA MD shows parts of the proteins falling apart. Please suggest. Thanks, Anirban[/quote] You probably use an mdp file that is for a more recent version of GMX. Did you try to use the one given in the tutorial and adapt it to your system?[file fg_protein.mdp, line unknown]:
Unknown left-hand 'rel_water' in parameter file

checking input for internal consistency...
calling /lib/cpp...

---

My system contains only multiple copies of a protein. So in what way should I chage the .mdp file that is given in the "reverse tutorial"? And if I continue with these warnings, then SA MD shows parts of the proteins falling apart.

Please suggest.

Thanks,

Anirban

anirbanzz wrote: Yes, I am using the same .mdp file give in the tutorial, but modified for my system. My mdp file looks like:

---

cpp = /lib/cpp
constraints = none
integrator = md
tinit = 0.0
dt = 0.002
nsteps = 40000
nstcomm = 0
nstxout = 1000
nstvout = 1000
nstfout = 1000
nstlog = 1000
nstenergy = 1000
nstxtcout = 1000
xtc_precision = 1000
nstlist = 10
energygrps = Protein
ns_type = grid
rlist = 0.9
coulombtype = Generalized-Reaction-Field
epsilon_rf = 62
rcoulomb = 1.5
rvdw = 1.0
Tcoupl = nose-hoover
tc-grps = Protein
ref_t = 300
tau_t = 0.1
Pcoupl = no
table_extension = 1.2


dihre = simple ; Some dihedrals are restrained for instance peptide bonds are set to trans conformation.
dihre_fc = 500
dihre_tau = 0.0
nstdihreout = 50

cap_force = 15000
cap_a = 100
fc_restr = 12000
r_CGW = 0.21
fc_restrW = 400
rel_steps = 0
rel_water = no


andersen_seed = 815131
annealing = single
annealing_npoints = 2
annealing_time = 0 60 ; CHANGE HERE -annealing control points for each group
annealing_temp = 1300 300 ; list of temperatures at control points for each group


gen_vel = yes
gen_temp = 1300
gen_seed = 473529
lincs_warnangle = 100

---

What should I change in it?

Thanks,

Anirban

anirbanzz wrote: I am using the modified version of Gromacs 3.3.1 (gromacs_reverse). But still it does not recognize these keywords.
It runs the other options well, like -coarse in mdrun. But grompp is throwing theses errors every time. How to solve this issue?

Thanks,

Anirban

anirbanzz wrote: Thanks again.
Sorry, but I think I am using the modified version of GROMACS only.
I did:

source /home/anirban/Software/GROMACS_CG/gromacs_reverse/bin/GMXRC
export GMXLIB=/home/anirban/Software/GROMACS_CG/gromacs_reverse/share/gromacs/top/
[anirban@anirban SIMANNEAL]$ which mdrun
~/Software/GROMACS_CG/gromacs_reverse/bin/mdrun

And still grompp gives these warnings !
Why is it happening so?

Thanks,

Anirban

anirbanzz wrote: Yes, I did use the full path of grompp. And still it does the same.
For grompp, I use:

/home/anirban/Software/GROMACS_CG/gromacs_reverse/bin/grompp -f fg_protein.mdp -c whole_protein_FG.gro -p topol_protein_fg.top -o try.tpr

and for mdrun (if I continie with grompp errors):

home/anirban/Software/GROMACS_CG/gromacs_reverse/bin/mdrun -coarse whole_protein_CG.gro -v -deffnm try

And mdrun is running fine. But should I continue, ignoring the grompp error?

Thanks,

Anirban

anirbanzz wrote: Thanks a lot.
Yes, I was using the Helsinki MARTINI workshop version. Now, after installing the latest version from the MARTINI website, the issue has been solved.

Thanks again,

Anirban