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

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 13 12:56:33 CEST 2010

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 

Per your genbox command below, if you have one hexane (in hexane_box.gro) and 
you add 200 (with -nmol), you should then have 201 hexane molecules in the system.

> 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.

Follow my previous advice and see if you can trace back where the error came 
from.  Count the molecules in your .gro file, i.e.:

grep OW hexane_solv.gro | wc -l

will give you the number of water molecules.  Do something analogous for hexane. 
  You're off by 2820 atoms, which is in the ballpark of 940 waters, so something 
has broken down pretty badly somewhere.


> ; 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


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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