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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