[gmx-users] Re: amount of solvent

shika pqah123 at gmail.com
Tue Oct 16 02:59:21 CEST 2012

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?


On Mon, Oct 15, 2012 at 6:05 PM, Justin Lemkul [via GROMACS]
<ml-node+s5086n5002026h90 at n6.nabble.com> wrote:
> On 10/14/12 10:41 PM, Nur Syafiqah Abdul Ghani wrote:
>> Dear All,
>> I would like to do the simulation between water and other solvent.
>> One question that i curious to know which is how i want to put the
>> amount of solvent, HFIP before i insert the water?
>> Its suppose 80% of HFIP and 20% of water.
>> But the starting point of my pdb already 1 nmol which only 1 compound of
>> HFIP.
>> So how can i insert the other amount of HFIP  before I insert the
>> water molecule?
> http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents
> -Justin
> --
> ========================================
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
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Best Regards,

Nur Syafiqah Abdul Ghani,
Theoretical and Computational Chemistry Laboratory,
Department of Chemistry,
Faculty of Science,
Universiti Putra Malaysia,
43400 Serdang,
alternative email : syafiqahabdulghani at gmail.com

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