There exists a (non-official) TEE-REX prototype for GMX 4 which allows full parallelization of each TEE-REX copy. Just contact ckut...@gwdg.de for more information.
Marcus > I would also add that you could also use TEE-REX which overcomes some of > the problems associated with normal REMD on large systems. Do note that as > far as i know the TEE-REX patch only works with GROMACS versions 3.3.x and > so each replica in the TEE-REX simulation can only be ran on one CPU, > meaning that these simulations can take a long time. > > Tom > > --On Friday, November 20, 2009 16:11:38 +0100 Berk Hess <g...@hotmail.com> > wrote: > >> Hi, >> >> I would think any system with a membrane in it is too large to gain much >> with REMD >> (unless you are interested in the temperature dependence). >> >> You can use essential dynamics sampling or flooding, see make_edi. >> >> Berk >> >>> Date: Fri, 20 Nov 2009 10:00:11 -0500 >>> From: jalem...@vt.edu >>> To: gmx-users@gromacs.org >>> Subject: Re: [gmx-users] Pushing MD further >>> >>> >>> >>> Thielges, Sabine wrote: >>> > Hi, >>> > >>> > I am currently running some GPRC MD with membrane. After a lot of >>> trial >>> > I now have a nice 25 ns run with an agonist. But the final structure >>> is >>> > too close the starting and I know it is far from what the biology >>> > describes. >>> > I would like to know if there is options that I can add to my md.mdp >>> > file to make the MD "explores some other area". >>> > >>> >>> There is no magic .mdp option to make sampling better, and you can not >>> necessarily ever trust the results of just one single simulation. There >>> are several options to enhance sampling: >>> >>> 1. Simulated annealing >>> 2. Replica-exchange MD >>> 3. Additional simulations with different starting velocities >>> >>> With #2, bilayers can be quite problematic. A recent paper from Max >>> Berkowitz's group in JPCB has a nice protocol for REMD with a >>> membrane. >>> >>> -Justin >>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> ======================================== >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >> >> >> __________________________________________________ >> Express yourself instantly with MSN Messenger! MSN Messenger > > > > ---------------------- > TJ Piggot > t.pig...@bristol.ac.uk > University of Bristol, UK. > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
