[gmx-users] Reg: Gromacs binary liquid-liquid simulation

[Florian Dommert]

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Check how many water atoms and hexane atoms are present in the gro file.
Then compare where differences arise. There are about 3000 atoms missing
in the top file so it seems the number of solvent or the number of
hexane molecules is wrong.

/Flo

On 09/13/2010 12:49 PM, vinothkumar mohanakrishnan wrote:
> i want to do MD for hexane-water system. I got hexane.gro and
> hexane..itp from PRODRG 2.5 Beta server with that i made the hexane.top
> file. below is the serious of commands i executed in gromacs, i am
> adding 200 hexane molecules an 1115 water molecules. after the first
> genbox i checked my topolgy file wheather the no .of hexane molecules
> got updated r increased to 200 but it doesn't and remains as 1 and then
> i maually changed it to 200 in the molecules section. i dont know where
> iam going wrong and i always get the error message as " number of
> coordinates in coordinate file (hexane_solv.gro, 7365) does not match
> topology (hexane.top, 4545) " while running grompp for energy
> minimisation. i read the error gromacs (website) documentation and found
> that the hexane.top r hexane.gro file is not getting updated, but iam
> helpless. any help is highly appreciated. below is my topology file as well.
> 
> ; The force field files to be included
> #include "ffG43a1.itp"
> 
> ; Include hexane topology
> #include "hexane.itp"
> 
> ; Include SPC water topology
> #include "spc.itp"
> 
> [ system ]
> hexane in Water
> 
> [ molecules ]
> ;molecule name number
> hexane         200
> SOL              1115
> *
> Commands*
> 
>  editconf -f hexane.gro -o hexane_box.gro -c -bt triclinic -box 8.31
> 3.01 3.01
> 
> genbox -cp hexane_box.gro -ci hexane_box.gro -p hexane.top -o
> hexane_multi.gro -nmol 200 -seed 1997
> 
> genbox -cp hexane_multi.gro -cs spc216.gro -p hexane.top -o hexane_solv.gro
> 
> grompp -f em.mdp -c hexane_solv.gro -p hexane.top -o hexane_em.tpr
> 
> Regards
> Vinoth
> 


- -- 
Florian Dommert
Dipl.-Phys.

Institute for Computational Physics

University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

Phone: +49(0)711/685-6-3613
Fax:   +49-(0)711/685-6-3658

EMail: dommert at icp.uni-stuttgart.de
Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
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