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 <[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 >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -Justin > > ====================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/ > > =====================_______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- 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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php