[gmx-users] Restraining bilayer/water system

Xavier Periole x.periole at rug.nl
Fri Mar 17 12:00:22 CET 2006

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 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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