[gmx-users] Restraining bilayer/water system

[Yang Ye]

The structure of the topology shall be

#include "ff"

;Beginning of molecule definition 1
[ moleculetype ]             -\
Mol1                          |
                              |---This is in one itp file
[ atoms ]                     |
...                          -/

[ position_restraints ] ;      ---This normally in another itp file.

;End of molecule definition 1

;Begin of Molecule definition 2
...
;End of molecule definition 2

[ system ]
; name
ABC

[ molecules ]
; name number
Mol1    1
Mol2    1

Yang Ye


Farid Sa'adedin wrote:
> 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 called.
>
> 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'
>
> TOP FILE:
>
> [ 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
> #endif
>
> [ 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?
>
>
> Yours,
>
> Farid
>