[gmx-users] Re: amount of solvent

[shika]

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?

Regards,
SHika

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
> 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/amount-of-solvent-tp5002006p5002026.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/amount-of-solvent-tp5002006p5002061.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.