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.
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. 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] > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
