Anthony Armstrong wrote:
Hello all,
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.
Are you sure you want to do this? All but one of your replicas become
non-physical and you can not do fun stuff like extracting kinetics info
from the trajectory anymore (see David van der Spoel and M. Marvin
Seibert: Protein Folding Kinetics and Thermodynamics from Atomistic
Simulations, Phys. Rev. Lett. 96 pp. 238102, 2006).
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.
The problem is in PME, for which you can not directly extract
interaction energies. There is a solution for this, but it is not
implemented.
Otherwise everything is present, except for some additional parameters
to determine your A and B functions.
Thanks,
Tony
Anthony A. Armstrong
Department of Biophysics and Biophysical Chemistry
Johns Hopkins University School of Medicine
725 North Wolfe Street
Baltimore, MD 21205
410-955-8715
410-955-0637 FAX
[EMAIL PROTECTED]
On Wed, 19 Jul 2006, Anthony Armstrong wrote:
Hello,
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.
Tony
Anthony A. Armstrong
Department of Biophysics and Biophysical Chemistry
Johns Hopkins University School of Medicine
725 North Wolfe Street
Baltimore, MD 21205
410-955-8715
410-955-0637 FAX
[EMAIL PROTECTED]
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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