>From reading the wiki, it seems like it is better to couple the entire system to one thermostat. Would this better? tc_grps = system
Thanks, JW On 10/11/07, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > Quoting JW Feng <[EMAIL PROTECTED]>: > > > Hello, > > > > This is a new warning that appears when executing version 3.3.2 of > > grompp to create a .tpr file. Should I be concerned? > > > > WARNING 1 [file aminoacids.dat, line 1]: > > T-Coupling group PROTEIN has fewer than 10% of the atoms (504 out of > > 24494) > > Maybe you want to try Protein and Non-Protein instead? > > WARNING 2 [file aminoacids.dat, line 1]: > > T-Coupling group CL- has fewer than 10% of the atoms (5 out of 24494) > > Maybe you want to try Protein and Non-Protein instead? > > > > My mdp options are: > > ;; TEMPERATURE COUPLING > > tcoupl = berendsen > > tc_grps = PROTEIN SOL CL- > > tau_t = 0.1 0.1 0.1 > > ref_t = 300 300 300 > > Don't couple solvent and ions separately. Merge them into one group with > make_ndx. > > http://wiki.gromacs.org/index.php/Thermostats > > -Justin > > > > > Thank you, > > > > JW > > > > -- > > Jianwen A Feng > > Center for Computational Biology > > Washington University in St. Louis > > _______________________________________________ > > gmx-users mailing list [email protected] > > 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://bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > ====================== > _______________________________________________ > gmx-users mailing list [email protected] > 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 > -- Jianwen A Feng Center for Computational Biology Washington University in St. Louis _______________________________________________ gmx-users mailing list [email protected] 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
