[gmx-users] segmentation fault with grompp

[Justin A. Lemkul]

I just used this topology in conjunction with popc128a.pdb (with some naming 
adjustments to match the topologies), and everything worked fine.  I am using 
version 4.0.5, as well.

Are you running grompp on a local workstation, or on a remote filesystem?  I 
have noticed sporadic, unpredictable seg faults in grompp which I presume are 
due to NFS blips on our cluster.

Have you recompiled without --enable-mpi, as I suggested before?  I don't know 
if that's the problem or not; do other systems (proteins in water, or something 
else reasonably simple) result in the same problem?

-Justin

Gard Nelson wrote:
> Ok, here's my topology file:
> 
> ; Include forcefield parameters
> #include "ffgmx.itp"
> #include "lipid.itp"
> 
> ; Include Lipid Topologies
> #include "popc.itp"
> 
> ; Include water topology
> #include "spc.itp"
> 
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
> #endif
> 
> ; Include generic topology for ions
> #include "ions.itp"
> 
> [ system ]
> ; Name
> Berger Membrane in water
> 
> [ molecules ]
> ; Compound        #mols
> POP               128
> SOL              2460
> 
> and here's my ff_dum.itp:
> 
> ; These constraints are used for dummy constructions as generated by 
> pdb2gmx.
> ; Values depend on the details of the forcefield, vis. bondlengths and 
> angles
> ; These parameters are designed to be used with the GROMACS forcefields
> ; ffgmx and ffgmx2 and with the GROMOS96 forcefields G43a1, G43a2 and G43b1.
> 
> ; Constraints for the rigid NH3/CH3 groups depend on the hygrogen mass,
> ; since an increased hydrogen mass translates into increased momentum of
> ; inertia which translates into a larger distance between the dummy masses.
> #ifdef HEAVY_H
> ; now the constraints for the rigid NH3 groups
> #define DC_MNC1 0.175695
> #define DC_MNC2 0.188288
> #define DC_MNMN 0.158884
> ; now the constraints for the rigid CH3 groups
> #define DC_MCN  0.198911
> #define DC_MCS  0.226838
> #define DC_MCC  0.204247
> #define DC_MCNR 0.199798
> #define DC_MCMC 0.184320
> #else
> ; now the constraints for the rigid NH3 groups
> #define DC_MNC1 0.144494
> #define DC_MNC2 0.158002
> #define DC_MNMN 0.079442
> ; now the constraints for the rigid CH3 groups
> #define DC_MCN  0.161051
> #define DC_MCS  0.190961
> #define DC_MCC  0.166809
> #define DC_MCNR 0.162009
> #define DC_MCMC 0.092160
> #endif
> ; and the angle-constraints for OH and SH groups in proteins:
> #define DC_CS  0.23721
> #define DC_CO  0.19849
> #define DC_PO  0.21603
> 
> Thanks for your help!
> Gard
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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