[gmx-users] Restraining bilayer/water system

Farid Sa'adedin fsaadedi at staffmail.ed.ac.uk
Thu Mar 16 16:34:55 CET 2006

Dear Users,

I have been trying to equilibrate a bilayer.  I have been able to 
restrain a bilayer in its own system using

#ifdef POSRES
#include "/home/tripos/lipid/dopc/minidopc/posre.itp"

in the topology file

define = -DPOSRES
in the steep, nvt and npt mdp files.

The problem occurs when I add water to the system and for some reason 
when I just want to restrain the
the bilayer GROMACS doesn't recognise the posre.itp file even though it 
becomes in the top.

#ifdef POSRES
#include "/home/tripos/lipid/dopc/minidopc/posre.itp" in water

This is the line I get when I run grompp:

cpp exit code: 256
cpp: too many input files
[tripos]dopc/minidopc$ Tried to execute: '/lib/cpp -I 
-I/usr/local/share/gromacs/top -DPOSRES dopc.top > grompptByAm1'

So as a result it doesn't restrain the lipids in the simulation.

If anyone has any ideas on how to just restrain a lipids with water in 
the system I would greatly appreciate them.

Yours sincerely,

Farid Sa'adedin--

Farid Sa'adedin
Membrane Biophysics Laboratory
Department of Veterinary Biomedical Sciences
College of Medicine & Veterinary Medicine
Royal (Dick) School of Veterinary Studies
University of Edinburgh
Edinburgh EH9 1QH

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