[gmx-users] Re: Fwd: How to can i replace a molecule

[Justin Lemkul]

On 10/7/12 9:17 PM, shika wrote:
> Thanks Justin.
>
> May I ask something, if i'm using the command for genbox before
> minimization which is
>
> genbox -cp protein_box.gro -cs solvent.gro -p control.top -o prot_solv.gro
>
> next i insert water by using same command;
>
> genbox -cp prot_solv.gro -p control.top -cs spc216.gro -o
> prot_solv_wtr.gro maxsol 350
>
> i'm using -cs for both genbox command instead of -ci -nmol, is it
> wrong to use the command like that?
>
>

I don't understand why you need two invocations of genbox, but syntactically the 
commands are correct.  The -ci -nmol options are for adding molecules randomly 
in the unit cell.  The -cs option is for stacking grids of water boxes (or 
whatever other solvent you provide) within the unit cell.

-Justin

>
>
> On Mon, Oct 8, 2012 at 8:59 AM, Justin Lemkul [via GROMACS]
> <ml-node+s5086n5001764h68 at n6.nabble.com> wrote:
>>
>>
>> On 10/7/12 3:52 PM, Ali Alizadeh wrote:
>>> Dear All users
>>>
>>> How to can i replace a molecule(for example methane) with another
>>> molecule(propane)?
>>> Number of these molecules are given and their position is random,
>>>
>>> Can I use genbox or genion, How to do i do it?
>>>
>>
>> Likely you can't, as you were already advised:
>>
>> http://lists.gromacs.org/pipermail/gmx-users/2012-October/075338.html
>>
>> A more robust approach for dealing with mixed systems can be found here:
>>
>> 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
>>
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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

========================================