Thank you Massimo sandal, Justin and mark , I also goes through the article and GMX archive. But I confuse with the protocol ( I am naive in REMD . So I want to conform protocol from the Expert and experience person )
I will be grateful to you for your suggestion. On Tue, Apr 2, 2013 at 6:45 PM, massimo sandal <deviceran...@gmail.com>wrote: > I would look on some paper which temperature ranges and conditions > (NPT/NVT) were used for systems of a similar size and with a similar aim. > > > 2013/4/2 rama david <ramadavidgr...@gmail.com> > > > 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? 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