[gmx-users] Re: amount of solvent

Justin Lemkul jalemkul at vt.edu
Tue Oct 16 15:32:10 CEST 2012

On 10/15/12 8:59 PM, shika wrote:
> Thanks all,
> I already pack the mixed solvent by using packmol cause the box that i
> used octahedron.Therefore the error that coming out is that topology
> and the gro file does not
> same. When I view the solvent by VMD  its just shows that the mixture
> only fill in the cubic form even though the starting box that i need
> was octahedron.
> So I would like to ask you guys if I already pack all the molecule,i
> need to create the new topology right? before start to minimize?

Since you need a topology to get a run input file, yes.  Your topology needs to 
match the coordinate file in terms of the number of each species present and the 
order in which they appear.



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


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