Dear all, I used the Stochastic dynamics (sd) integrator for single molecule in gas phase for around 80 ns (I need this for bonding parameter course-grained particularization using votca), would you please have a look at the sturcure before and after SD, and help me underestand why this happens? And how one can avoid that. And also, if it is necessary to use SD in this step of CG parameterization if you are familiar with votca by chance.
https://drive.google.com/open?id=1pKkEzyo4KkIcBv-hPexohMUAZpNnTAjy https://drive.google.com/open?id=1RfVqan27GCPyOi6m1dcpmaFXBzFvPVVy Thank you. Best regards, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
