On Thu, Nov 1, 2012 at 8:45 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/1/12 4:36 PM, Steven Neumann wrote: >> >> Dear Gmx Users, >> >> I have system with protein in water. I equlibrated it in at 300 K and >> 1 bar for 5 ns with position restrained of protein heavy atoms. I run >> script at NP and increasing temperature from 300K to 600 K with >> changing temperature of 1 Kelvin every 1000 steps. Then temperaure is >> set to be 600 K for another 4 ns to cool it down after to 300K within >> 2 ns. >> >> System fails when the temperature reached 600K - my box is being >> expanded during the temperature increase TWICE! This is why it fails >> and my job terminates. >> Would you suggest something? >> > > A complete .mdp file would be useful here (just in case), although the > observed behavior doesn't sound too unusual to me. Under constant pressure, > when you heat a liquid, what happens? 600K is well above the boiling point > of water, so it sounds to me like your unit cell is simply responding to > what you're doing. Perhaps you should be using NVT, but I don't know what > your purpose for this procedure is. > > -Justin
Thanks for your reply. I am trying to get parametrs for coarse grained model so I want to repeat this procedure until covergence. Do you think NVT could be used for this purpose? Steven > > -- > ======================================== > > 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