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

vinothkumar mohanakrishnan kmvinoth at gmail.com
Mon Sep 13 12:49:50 CEST 2010

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

 editconf -f hexane.gro -o hexane_box.gro -c -bt triclinic -box 8.31 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

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