Dear friends , Thank you justin and Mark for your suggestion I increases my temp range from 310-360 K Now I get 20 replicas .
Is in such large temp range wlll it be good to use NPT. Would you tell me the temp differences in which box instability generally arises .. Is my working-flow right or need to change much Thank you With Best Regards.. On Tue, Apr 2, 2013 at 5:08 PM, Erik Marklund <er...@xray.bmc.uu.se> wrote: > > On 2 Apr 2013, at 13:30, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > On 4/2/13 7:13 AM, rama david wrote: > >> Dear friends, > >> I am naive to the Replica exchange Molecular dynamics ( REMD). > >> I have plan to use REMD for temp. 310-320 K to my system. > >> I thoroughly search the Mailing-list Archive for the REMD problem. > >> It was a really helpful to start. > >> > >> My system consist of peptide + water. > >> > >> I used the following work-flow, Would you please help me to find out > >> my mistakes... > >> > >> 1. energy minimesation for peptide + solvent > >> 2. Different Mdp file for temp. ( 4 temp therefore 4 mdp file ) > >> 3. Make tpr file for each nvt run > >> 4. Then separate equilibration for each temp ( 4 equilibration steps ) > >> 5. Then made NPT.mdp file for each temp ( 4 temp ) > >> 6. Then again equilibration for NPT at 4 temp.( 4 equilibration steps ) > >> 7. Then run md production with -replex 1000 -multi 4 command .. > >> > >> To determine the temp I used web-server http://folding.bmc.uu.se/remd/ > >> > >> Please suggest me any improvements that are possible to implement in > >> my work flow. > >> > > > > Such a narrow range of temperatures defeats the purpose of using REMD. > Normally, a much larger range is used over many more simulations. For > near-ambient temperatures, NPT can be used, but if you include much higher > temperatures, you should use NVT due to box instability upon exchanges. > > > > -Justin > > Sure, the enhanced sampling is basically gone, but you can deduce > temperature dependences from such simulations and to some extent benefit > from the mixing, can't you? > > Erik > > > > > -- > > ======================================== > > > > Justin A. Lemkul, Ph.D. > > Research Scientist > > 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/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 > > -- > 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/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 > -- 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/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