[gmx-users] Restraining bilayer/water system

[Yang Ye]

You shall append those three lines just under the definition of the 
lipid molecule. You may paste your top file for us to comment.

Yang Ye

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"
> #endif
>
> 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
> #endif
>
> 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
> Summerhall
> Edinburgh EH9 1QH
> SCOTLAND
>
>
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