[gmx-users] Generating a solvent box

[David van der Spoel]

Dilraj Lama wrote:
> 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.

just do md with pressure coupling.
> 
> 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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> 
> 


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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