[gmx-users] Re: amount of solvent

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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