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
