On 14/08/2012 1:07 AM, Sai Pooja wrote:
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.
Manual 7.3.3 says how.
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.
If you contact the authors, they may be willing to share an .mdp file
with you. Even if they do, you doing some careful reading of manual 7.3
is in order. Attempting to reproduce some old results is likely to be a
good idea.
Mark
--
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
