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

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 13 12:28:01 CEST 2010

Please keep all Gromacs-related correspondence on the gmx-users list.  I am not 
a private tutor.  I am CC'ing the message to the list and I would ask that you 
keep all further discussion going there.

There is a mismatch between your .top and .gro, but what it is I cannot say. 
Determine how many molecules of hexane and water have been added by the commands 
you gave below; these numbers should be assigned in the [molecules] section of 
the .top file.


vinothkumar mohanakrishnan wrote:
> Dear Justin
> I am vinoth currently doing my Ph.D in India (at IIT Madras). I am 
> working on molecular dynamics of liqud-liquid interfaces using GROMACS 
> 4.0. I found in the gromacs users list that you answer many questions 
> and thereby helpingg the others to find the solutions. I have certain 
> doubts and i hope you will clarify that.
> *My problem*: 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, 
> and 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. hope you will help me in finding a solution.
>  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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