[gmx-users] Restraining bilayer/water system

Farid Sa'adedin fsaadedi at staffmail.ed.ac.uk
Fri Mar 17 12:22:04 CET 2006

Dear Xavier,

My posre.itp file represents one lipid molecule.  My p1.itp represents 
1 water molecule.

I made new itp files using genpr defining one lipid molecule and water 
molecule called POSRE_L.itp and POSRE_W.itp as you suggested them to be 

The strange thing is that I can restrain the lipids when there is no 
water in my system.  But when I add water to the system, grompp doesn't 
seem to restrain the lipids anymore.  It brings up this message:

>> 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'


[ system ]
; name
DOPC in water

#ifdef POSRES
#include "/home/tripos/lipid/dopc/minidopc/POSRE_L.itp" in water
;#include "/home/tripos/lipid/dopc/minidopc/POSRE_W.itp" in water

[ molecules ]
; name number

DOPC    18

SOL              1463

As you can see from my top file everything is in order. I define the 
lipid and water seperately in the top file.  But how can I define them 
seperately in my mdp file?



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

Quoting Xavier Periole <x.periole at rug.nl>:

> fsaadedi at staffmail.ed.ac.uk wrote:
>> Dear Xavier,
>> I have put the posre.itp file in the order that you mentioned and I 
>> have a file which has postional restraints on one water molecule.
>> (See previous email below)  So it is not an ordering problem.
>> If anyone has any suggestions why grompp isn't restraining just the 
>> lipid molecules in my bilayer/water system I would greatly 
>> appreciate it.
>> The posre itp file represents one lipid molecule and the p2.itp file 
>> represents all water molecules.
>> I have a p1.itp file that represents one water molecule but this 
>> also brought up the :
>> 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'
>> message.
>> #include "/home/tripos/lipid/ffgmx2_lipid.itp"
>> #include "/home/tripos/lipid/DOPCHT.itp"
>> #include "/usr/local/share/gromacs/top/spc.itp"
> Did you try to define one POSRES flag for the water and one for the lipids.
> I mean one call POSRE_W the other POSRE_L and then define
> then in the mdp file and call them separatelly at their respective places ?
> Not together, but in the itp of the lipid and itp of the water ?
> XAvier
> -- 
> ----------------------------------
>  Xavier Periole - Ph.D.
>  Dept. of Biophysical Chemistry / MD Group
>  Univ. of Groningen
>  Nijenborgh 4
>  9747 AG Groningen
>  The Netherlands
>  Tel: +31-503634329
>  Fax: +31-503634398
>  email: x.periole at rug.nl
>  web-page: http://md.chem.rug.nl/~periole
> ----------------------------------
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