[gmx-users] Re: add more solvent?

[shika]

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
>> water.
>> 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:
>
> http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents
>
> -Justin
>
> --
> ========================================
>
> 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
>
> ========================================
> --
> gmx-users mailing list    [hidden email]
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to [hidden email].
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> ________________________________
> If you reply to this email, your message will be added to the discussion
> below:
> http://gromacs.5086.n6.nabble.com/add-more-solvent-tp5003568p5003569.html
> To start a new topic under GROMACS Users Forum, email
> ml-node+s5086n4370410h94 at n6.nabble.com
> To unsubscribe from GROMACS, click here.
> NAML



-- 
Best Regards,

Nur Syafiqah Abdul Ghani,
Theoretical and Computational Chemistry Laboratory,
Department of Chemistry,
Faculty of Science,
Universiti Putra Malaysia,
43400 Serdang,
Selangor.
013-7188131
alternative email : syafiqahabdulghani at gmail.com




--
View this message in context: http://gromacs.5086.n6.nabble.com/add-more-solvent-tp5003568p5003570.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.