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
