[gmx-users] REST variant of REMD
armstron at queen.med.jhmi.edu
Mon Jul 24 20:45:03 CEST 2006
I'd like to run REMD on a peptide system, but it turns out out my
system is a little to large, and I've determined that to get a swap
probablity of .2, a separation of temperature of only a couple degrees
between replicas would be required. I ran across the paper of Liu et al.
(PNAS 2005 102:13749-13754) on Replica Exchange with Solute Tempering
which addresses this problem and which appears to attempt temperature
swaps based on a "modified" total potential in which solute/solute and
solute/protein interactions are first scaled.
My question is:
How might I go about calculating a user defined energy (in this case
E(X) = Ep(X) + A(T) * Ew(X) + B(T) * Epw --> where X is the set of
system coordinates, subscripts p, w, and pw denote protein/protein,
water/water, and protein/water interactions, respectively, and A(T) and
B(T) are scale factors involving the target temperature for the given
replica) and then pass this energy rather than the unscaled potential
to gromacs for determining whether or not to swap temperatures.
Any help would be much appreciated.
Anthony A. Armstrong
Department of Biophysics and Biophysical Chemistry
Johns Hopkins University School of Medicine
725 North Wolfe Street
Baltimore, MD 21205
armstron at groucho.med.jhmi.edu
On Wed, 19 Jul 2006, Anthony Armstrong wrote:
> I'm hoping to get some tips on removing protein rotation inside a
> triclinic water box. Apologies if this has been covered recently, but
> the most recent discussion I've been able to track down is a thread from
> 2003 which stated a patch was available to prevent such rotations and an
> algorithm would be formally implemented into GROMACS "in the near future"
> (Tsjerk Wassenaar t.a.wassenaar at chem.rug.nl Tue May 20 13:52:00 CEST
> 2003). Has the implementation occurred? If I use comm-grps = Protein and
> comm-mode = angular? Of course I'm in the process of trying it, but
> thought some kind person from the Gromacs community might be able to save
> me some time if it is going to fail. Thanks in advance.
> Anthony A. Armstrong
> Department of Biophysics and Biophysical Chemistry
> Johns Hopkins University School of Medicine
> 725 North Wolfe Street
> Baltimore, MD 21205
> 410-955-0637 FAX
> armstron at groucho.med.jhmi.edu
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