Dear gromacs users, I perform membrane-protein simulation and used the same mdp files as suggested by the tutorial of Dr. Justin Lemkul with one exception of changing the correct parameters for charmm36ff as suggested by gromacs manual.
I performed 10ns of *NVT equilibration with position restrained* on the protein and found a convergence of the temperature to the desired temperature. Followed by 50ns of *NPT equilibration with position restrained *on the protein, and after that, I performed 100ns of *NPT equilibration without position restraint*. My question is, in the *NPT equilibration without the position restrain,* what should I put in the category of *refcoord_scaling? com? *or should I delete it as I found in the MD.mdp file in the tutorial? Thanks in advance, Olga -- 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.
