[gmx-users] Reg: Adding multiple molecules

[vinothkumar mohanakrishnan]

Hi Justin

Thank you for your suggestion.

Regards
Vinoth

On Mon, Sep 27, 2010 at 4:52 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> vinothkumar mohanakrishnan wrote:
>
>> Hi justin
>>
>> if genbox is not able to find sufficient space then why should one
>> calculate number density for the given box dimension?.similarly the  the
>>
>
> Just because you can calculate a certain number density does not
> necessarily mean that the algorithm genbox is using can produce such a
> configuration.  It inserts molecules randomly, so you may be able to find a
> magical value of -seed for which this will work.  The simpler approach is
> what I suggested earlier.
>
>  number of molecules are not getting updated in the molecules section of
>> the topology file when inserting multiple molecules using the genbox
>> command. everytime i need to update it manually.is <http://manually.is>
>> there a way to update it automatically?
>>
>>
> The topology will only be updated automatically when adding water.
>  Otherwise, you have to do it yourself.
>
> -Justin
>
>  Regards
>> Vinoth
>>
>>
>> On Mon, Sep 27, 2010 at 4:31 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    vinothkumar mohanakrishnan wrote:
>>
>>        Hi all
>>
>>        I have a diffculty in adding multiple molecules of hexane to my
>>        box. my box size is 4.72*2.36*2.36 (nm) according to my number
>>        density calculations the box should fit 124 molecules of hexane
>>        whereas it adds only 76 molecules to the box below is my
>>        command. i had evev tried with -try command but without sucess.
>>
>>        genbox -cp hexane-box.gro -ci hexane.gro -p hexane.top -o
>>        hexane-multi.gro -nmol 124 -seed 1268
>>
>>
>>    If you're not getting all the molecules you want, then genbox is
>>    unable to find sufficient space for them.  Try a larger box, then
>>    equilibrate.
>>
>>    -Justin
>>
>>        Regards
>>        Vinoth
>>
>>
>>    --     ========================================
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>
>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
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>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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