Re: [gmx-users] Replica Exchange MD ... Exchange rates
Carsten Baldauf wrote: dear gromacs-users// what would you think are good exchange rates between the replicas in a REMD? :-) I'm about to submit a paper partly on this topic... the short answer is that most people publishing REMD exchange rates have one that is a good deal lower. There's literature that recommends 20%, but a lot of people are in the 10-30% range. If you get rates that seem too low, then the first thought is to decrease the period between exchange attempts in order to increase the exchange rate per unit simulation time, but there's published data (e.g. from Periole Mark, J. Chem. Phys this year) that indicates that there are lower limits below which this is ineffective. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Replica Exchange MD ... Exchange rates
That's great. Usually is 30%, of course also depends on how often you let exchange. Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Carsten Baldauf Sent: Tuesday, July 10, 2007 5:43 PM To: Discussion list for GROMACS users Subject: [gmx-users] Replica Exchange MD ... Exchange rates dear gromacs-users// what would you think are good exchange rates between the replicas in a REMD? something like this? Replica exchange statistics Repl 499 attempts, 250 odd, 249 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 Repl .40 .48 .53 .55 .54 .56 .53 .57 .55 .58 .57 .60 .63 .61 .60 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl 101 133 131 136 137 142 125 147 142 137 141 151 168 152 153 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl .40 .53 .52 .55 .55 .57 .50 .59 .57 .55 .56 .61 .67 .61 .61 or lower? thanks in advance// carsten ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Replica Exchange MD ... Exchange rates
From: Mark Abraham [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] Replica Exchange MD ... Exchange rates Date: Tue, 10 Jul 2007 20:15:31 +1000 Carsten Baldauf wrote: dear gromacs-users// what would you think are good exchange rates between the replicas in a REMD? :-) I'm about to submit a paper partly on this topic... the short answer is that most people publishing REMD exchange rates have one that is a good deal lower. There's literature that recommends 20%, but a lot of people are in the 10-30% range. If you get rates that seem too low, then the first thought is to decrease the period between exchange attempts in order to increase the exchange rate per unit simulation time, but there's published data (e.g. from Periole Mark, J. Chem. Phys this year) that indicates that there are lower limits below which this is ineffective. I would agrue this quantity by itself is irrelevant. Also I think you can not call this a rate, it is a probability. The rate (exchanges per unit of time) is already a much more relevant quantity. But even there the average does not say much. What matters in the end is that the different replicas sample the whole temperature space in a reasonable way. This can not be judged from the probabilities. I would say that in general 30% is on the high side, you could save yourself computer time, or increase the sampling by choosing larger temperature differences. But again, you have to make sure exchange happens regular enough between all temperature pairs. Berk. _ Play online games with your friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
