[gmx-users] Restraining bilayer/water system
leafyoung81-group at yahoo.com
Thu Mar 16 18:13:21 CET 2006
You shall append those three lines just under the definition of the
lipid molecule. You may paste your top file for us to comment.
Farid Sa'adedin wrote:
> 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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