[gmx-users] Generating a solvent box

[Dilraj Lama]

Hello justin,
             Here is what I did.I initially defined a cubic box into which
I placed the TFE molecule.This I did using editconf.Then I
used genconf with the follwing command.

 genconf_mpi -f tfe-box-four.gro -o out-four.pdb -nbox 5 5 5

Yes I am able to generate a regular arrangment of the TFE molecules.

But what I want to do now is to have a predfined cubic box dimension which
I want to solvate with a fixed number of TFE molecules corresponding to a
given density.

Thanks for your response.
> Quoting Dilraj Lama <dennis at iitk.ac.in>:
>
>> Hello gmx users,
>>                 I have a query to ask.It would be nice if someone could
>> suggest me on this.I have a tfe molecule generated using
>> InsightII program package.Now I would like to create a box
>> containing a fixed number of tfe molecules based on its
>> density.I tried using "genbox" and "genconf" for the
>> purpose but am not able to achieve my aim.If someone has
>
> What did you try (i.e., what commands did you issue)?  You should be able
> to
> generate at least a regular arrangement of TFE molecules with genconf.
>
>> tried to do this before and have some idea, I would be
>> thankfull if you could shed some light on the subject.
>>
>> Thanking you.
>> --
>> Dilraj Lama,
>> Graduate student,
>> Bioinformatics and Biomolecular Simualtion lab,
>> Dept. of BSBE;IITK-kanpur,
>> Uttar pradesh,India-208016.
>> email:dennis at iitk.ac.in,dilraj2002 at yahoo.com
>> mob:09415473973
>>
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>
> -Justin
>
> ====================Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul at vt.edu | (540) 231-9080
> http://bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
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-- 
Dilraj Lama,
Graduate student,
Bioinformatics and Biomolecular Simualtion lab,
Dept. of BSBE;IITK-kanpur,
Uttar pradesh,India-208016.
email:dennis at iitk.ac.in,dilraj2002 at yahoo.com
mob:09415473973