[gmx-users] Re: add more solvent?
pqah123 at gmail.com
Fri Dec 7 02:28:44 CET 2012
Thanks Justin for your reply.
Means that i need to run two times command for genbox?
is it possible?
Allright then I'll try it first
On Fri, Dec 7, 2012 at 9:25 AM, Justin Lemkul [via GROMACS]
<ml-node+s5086n5003569h23 at n6.nabble.com> wrote:
> On 12/6/12 8:22 PM, Nur Syafiqah Abdul Ghani wrote:
>> Dear Users,
>> May I know after do the command
>> genbox -cp prot_box.gro -ci solvent.gro -nmol 2000 -cs spc216.gro -p
>> control.top -o prot_mix_sol.gro
>> the result shows,
>> Output configuration contains 1121788 atoms in 367835 residues
>> Volume : 11420.4 (nm^3)
>> Density : 1007.84 (g/l)
>> Number of SOL molecules: 365793
>> I need to put the solvent mix with water with ratio approximately 80%
>> of solvent : 20% water.
>>>From here after i done the calculation its only give 5% of solvent in
>> Therefore my question is,can i add another -nmol of solvent without
>> insert the -cs anymore?
>> Hope you guys already facing the same problem like i do.
> The best approach is to do it in two steps:
> 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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Nur Syafiqah Abdul Ghani,
Theoretical and Computational Chemistry Laboratory,
Department of Chemistry,
Faculty of Science,
Universiti Putra Malaysia,
alternative email : syafiqahabdulghani at gmail.com
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