Thanks for providing the insight about it. I have tried it. I have two query.. (1) As in the case of simulation with urea as a solute and water as solvent the corresponding file urea+h2o.gro file is given there.I have to do simulation similar to urea i.e. guanidium ion as a solute in place of urea.So in that case how will i be able to create Gdm+h2o.gro file analogous to urea+h2o.gro(Gdm=Guanidium ion).
(2) If i have to perform simulation with varying concentration of system(Guanidium & water), so how will i be able to do it.As i have seen in case of urea+h2o.gro concentration of system is fixed and if i have to generate a system of different molal(different ratio of urea and water), so will be play with concentration. If any help i will be getting, i will be very thankful. kinshuk raj srivastava IIT-Bombay India Quoting [EMAIL PROTECTED]: > >> >> >> Hi all, >> I have been try to put up MD simulation of guanidium chloride >> simulation >> in SPC water model.I have been facing problem regarding *.rtp, *.itp >> file generation for new entry for guanidium ion.If any one is aware >> about how to create above mentioned file please let me give some insight >> about file corresponding guanidium ion. >> I tried to make it with argenine side chain but i have been facing >> problem while generating above mentioned file. > > http://wiki.gromacs.org/index.php/Parameterization > > You could use PRODRG to generate the topology, but you will have to > validate the > parameters (see the above link), especially the charges that PRODRG > assigns. > They are often unsatisfactory. > > -Justin > >> >> >> kinshuk raj srivastava >> IIT-Bombay >> Mumbai, India >> >> >> _______________________________________________ >> 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 A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > [EMAIL PROTECTED] | (540) 231-9080 > http://www.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 > _______________________________________________ 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