[gmx-users] segmentation fault with grompp

[Gard Nelson]

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
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