[gmx-users] implicit solvent protein simulations with charmm

Sai Pooja saipooja at gmail.com
Mon Aug 13 17:07:18 CEST 2012


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.


reference: Bjelkmar et. al., JCTC (2010)

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