Hi, I have read a couple of posts on related topics but I am still not sure how to proceed and would be grateful to get some help.
I want to run implicit solvent simulations of a protein+water (implicit) system in the canonical ensemble using charmm27+cmap forcefield. I am trying to use the parameters used in the 2010 JCTC paper on the implementation of charmm in gromacs. In this paper, it seems that Stochastic Dynamics with zero cut-off is used for the implicit solvent system. Moreover, the inverse friction constant is specified as 91 ps-1. It is not clear to me how does one specify this inverse friction constant with the "sd" integrator in gromacs. Does it correspond to "mass/tau_t" or the bd_fric (which I understand is used with the "bd" integrator)? If this is infact equal to mass/tau_t, what tau_t value does it correspond to (18/tau_t = 91)? The paper also claims to be able to use a time step of 5fs with OBC+virtual sites. Again, I would like to find out the right set of parameters that would allow this time-step. Regards, Sai reference: Bjelkmar et. al., JCTC (2010) -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
