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 <[EMAIL PROTECTED]>:
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:[EMAIL PROTECTED],[EMAIL PROTECTED]
mob:09415473973
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====================Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (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
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