Re: [gmx-users] mdp file for 370 K MD based on Justin's tutorial
You haven't adjusted the temperature on the production mdp file, it's still 300 K. J On Mon, May 22, 2017 at 12:37 PM, ZHANG Cheng <272699...@qq.com> wrote: > Dear Gromacs, > I am performing 370 K MD based on Justin's tutorial. > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > gmx-tutorials/lysozyme/index.html > > > After "Step Five: Energy Minimization", I need to do NVT, NPT and a > production run. > > > I think I need to change 300 K to 370 K in three mdp files. Specifically, > > > 1) In the NVT: > ref_t = 370 370 ; reference temperature, one for each group, in > K > gen_temp = 370 ; temperature for Maxwell distribution > > > > 2) In the NPT: > ref_t = 370 370; reference temperature, one for each group, in K > > > 3) In the production run: > ref_t = 300 300 ; reference temperature, one for > each group, in K > > > Can I ask if these are the adjustments I need to do, and if there are > something else I need? Thank you. > > > Yours sincerely > Cheng > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdp file for 370 K MD based on Justin's tutorial
Dear Joao, Sorry, I forgot. Thank you for reminding me. Is that all right now? Is that true that NVT needs to change two lines, while NPT and production run only need to change one line? Yours sincerely Cheng 1) In the NVT: ref_t = 370 370 ; reference temperature, one for each group, in K gen_temp = 370 ; temperature for Maxwell distribution 2) In the NPT: ref_t = 370 370; reference temperature, one for each group, in K 3) In the production run: ref_t = 370 370 ; reference temperature, one for each group, in K -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdp file for 370 K MD based on Justin's tutorial
On 5/22/17 6:47 AM, ZHANG Cheng wrote: Dear Joao, Sorry, I forgot. Thank you for reminding me. Is that all right now? Is that true that NVT needs to change two lines, while NPT and production run only need to change one line? Yes. -Justin Yours sincerely Cheng 1) In the NVT: ref_t = 370 370 ; reference temperature, one for each group, in K gen_temp = 370 ; temperature for Maxwell distribution 2) In the NPT: ref_t = 370 370; reference temperature, one for each group, in K 3) In the production run: ref_t = 370 370 ; reference temperature, one for each group, in K -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
