Re: [gmx-users] REMD equilibration
On 03/23/2012 10:41 AM, francesco oteri wrote: Dear gromacs users, I have to perform REMD simulation, but since it is the first time I apply this tecnique I have a question regarding system equilibration. As far as I know, befaore starting the REMD each replica has to be equlibrated. The equilibration has to be carried out in the NPT ensemble or only in the NVT? Depends on the ensemble you want to simulate. If the replica you are interested in should be simulated in NVT you should equilibrate this replica well and take care that all replicas have the same volume (meaning that the replicas with higher T have very high pressures). You also can simulate each replica in an NPT ensemble (and also equilibrate the replicas with NPT). When the pressure is included in the Metropolis criteria for the exchange of the trajectories. Thanks in advance, Francesco all the best Sebastian -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] REMD equilibration
Hi Francesco, It should be the same ensemble, in which you want to carry out the production REMD. Andreas From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of francesco oteri Sent: 23 March 2012 09:41 To: Discussion list for GROMACS users Subject: [gmx-users] REMD equilibration Dear gromacs users, I have to perform REMD simulation, but since it is the first time I apply this tecnique I have a question regarding system equilibration. As far as I know, befaore starting the REMD each replica has to be equlibrated. The equilibration has to be carried out in the NPT ensemble or only in the NVT? Thanks in advance, Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] REMD equilibration
I understand, I am planning to run REMD between 300 and 600 K, so I think it is better equlibrating in NVT ensemble because at high temperature water evaporates, is it? Francesco Il giorno 23 marzo 2012 10:53, Kukol, Andreas a.ku...@herts.ac.uk ha scritto: Hi Francesco, It should be the same ensemble, in which you want to carry out the production REMD. Andreas From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of francesco oteri Sent: 23 March 2012 09:41 To: Discussion list for GROMACS users Subject: [gmx-users] REMD equilibration Dear gromacs users, I have to perform REMD simulation, but since it is the first time I apply this tecnique I have a question regarding system equilibration. As far as I know, befaore starting the REMD each replica has to be equlibrated. The equilibration has to be carried out in the NPT ensemble or only in the NVT? Thanks in advance, Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] REMD equilibration
francesco oteri wrote: I understand, I am planning to run REMD between 300 and 600 K, so I think it is better equlibrating in NVT ensemble because at high temperature water evaporates, is it? Another very real concern is the stability of the simulations under NPT. At higher temperatures, the box itself may vary more widely and when the system is exchanged, the algorithms can fail. This phenomenon has been reported by a number of other users. With NVT, this does not happen. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] REMD equilibration
23 mar 2012 kl. 11.37 skrev Justin A. Lemkul: francesco oteri wrote: I understand, I am planning to run REMD between 300 and 600 K, so I think it is better equlibrating in NVT ensemble because at high temperature water evaporates, is it? Another very real concern is the stability of the simulations under NPT. At higher temperatures, the box itself may vary more widely and when the system is exchanged, the algorithms can fail. This phenomenon has been reported by a number of other users. With NVT, this does not happen. -Justin Very true. The benefit from NPT is on the other hand that the replicas can be more distant in temperature space, so if it works then NPT is more efficient. Erik -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
