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

[shika]

it is because when i put

genbox -cp protein_box.gro -ci solvent.gro -nmol 1381 -p control.top
-o prot_solv.gro

the error turn out like this :

System total charge: 0.000
Grid: 17 x 16 x 14 cells
nri = 12718, nrj = 100152
Try 9119box_margin = 0.45overlap:
Killed

thats why i need to run genbox twice

On Mon, Oct 8, 2012 at 9:21 AM, Justin Lemkul [via GROMACS]
<ml-node+s5086n5001768h92 at n6.nabble.com> wrote:
>
>
> 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]
>> <[hidden email]> 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
>
> ========================================
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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,
Selangor.
013-7188131
alternative email : syafiqahabdulghani at gmail.com




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