[gmx-users] change of bilayer structure during NVT equilibration

shahab shariati shahab.shariati at gmail.com
Sun Oct 6 16:57:50 CEST 2013

Dear Justin

Very thanks for your quick reply.

> Depends on how you prepared the system.

For initial structure of system, I used coordination from website:

> Probably there were voids in the solvent or lipid headgroups that caused
> distortion in the system.

When I see the initial structure of system by VMD, There is no voids in the
solvent or lipid headgroups, apparently.

> Restraints on the lipid headgroups along z could help.

I want use restraints on the dopc and chol molecules (lipid molecules). For this

purpose, I did following:

1) I used genrestr tool twice. genrestr gave me 2 files (lipidchol.itp and
lipiddopc.itp for cholesterol and dopc molecules, respectively).

2) I added define = -DPOSRES in mdp file.

3) I added Include Position restraint file to the topology file.

My topology file is as follows:

; Include forcefield parameters
#include "gromos-43a1-s3_lipid.ff/forcefield.itp"

#include "cholesterol.itp"

; Include Position restraint file
#ifdef POSRES
#include "lipidchol.itp"

#include "dopc.itp"

; Include Position restraint file
#ifdef POSRES
#include "lipiddopc.itp"

#include "gromos-43a1-s3_lipid.ff/spc.itp"

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000

#include "gromos-43a1-s3_lipid.ff/ions.itp"

[ system ]
; Name

[ molecules ]
; Compound        #mols
CHOL        26
DOPC       102
SOL       1706
When I used grompp, I encountered error:

Fatal error:
[ file lipidchol.itp, line 34 ]:
Atom index (30) in position_restraints out of bounds (1-29).
This probably means that you have inserted topology section
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.
How to fix this issue?

Best wishes

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