[gmx-users] Re: Coarse grain simulation

Justin A. Lemkul jalemkul at vt.edu
Mon Feb 22 13:59:45 CET 2010

Sarath Kumar wrote:
> I m trying to reproduce the same thing, by following the tutorial.
> i m trying to learn the coarse grain simulation with their files, so 
> that i can apply for my protein.
> Starting with lipids, as per their tutorial
> I m just doing the steps in that tutorial, with their files,
> after the genbox,
> genbox -ci dspc_single.gro -nmol 128 -box 7 7 7 -try 100 -o 128_noW.gro
> grompp
> grompp -f em.mdp -c 128_noW.gro -p dspc.top -maxwarn 10
> shows the error, number atoms doesnt match,as
> Fatal error:
> number of coordinates in coordinate file (128_noW.gro, 1400)
>              does not match topology (dspc.top, 1792)

It looks like you should only have DSPC lipids in the box (from genbox), and 
nothing else, is that correct?  Then the topology is specifying something else. 
  Did you generate the .top yourself, or are you using one from the tutorial's 
site?  If you downloaded it, it may already contain water.  Have a look into the 
topology to see what it expects.



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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