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

[Justin Lemkul]

On 10/8/12 12:48 AM, shika wrote:
> 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
>

Sorry, read the original message too quickly and thought the solvent 
configuration was the same both times.  My mistake :)

The error you receive is a result of genbox failing to do what you're asking. 
You've exhausted the memory available, suggesting that there is no way to add 
that many molecules of whatever solvent into the box.  Either set a larger box 
with editconf prior to this step, or try to insert fewer molecules.

-Justin

> 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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>
>
>

-- 
========================================

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

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