Hi Kiana, I always heat from 5 K to 300 K with ref_t=300 (ending temp) and gen_temp=5 (starting temp). 5 K is as good as starting at 0 K for my systems. Hope that helps.
Regards, On Wed, Dec 4, 2013 at 12:18 PM, kiana moghaddam <ki_moghad...@yahoo.com>wrote: > Dear Jastin > > Thanks very much for your reply, when I heat system from 0 to 300 K with > simulated annealing, ref_t =300 is correct? > > Best Regards > > > > On Tuesday, December 3, 2013 5:53 PM, Justin Lemkul <jalem...@vt.edu> > wrote: > > > > On 12/3/13 2:17 AM, kiana moghaddam wrote: > > Dear GMX Users > > > > I want to run NVT equilibration and NPT equilibration (after NVT) and > want to increase temperature gradually i.e. from 0 to 300 K over 100 ps, > but I have some questions about this process: > > when I use simulated annealing in NVT as following > > annealing_time = 0 15 30 45 60 80 100 > > annealing_temp = 0 50 100 150 200 250 300 > > I don't know how to change gen_temp. Should gen_temp be 0 or 300 K? > > > > Generating velocities and then immediately freezing (in the strictest of > sense) > the system is likely not going to be stable or effective because the > thermostat > will go haywire trying to compensate for such a drastic change in > temperature. > It is an interesting question, because how does one generate velocities at > 0 K? > Theoretically, there are none. I would suggest setting gen_temp to 0; > you can > check the .tpr (via gmxdump) to see if any velocities are present, but > even if > they are they should be very small and largely irrelevant. The annealing > protocol will warm the system relatively quickly, so even after a few > dynamics > steps, you will have small velocities within the system. > > > > At the first time, I did not use simulated annealing. I prepared 7 mdp > files that in the first mdp file, I set nsteps=0, gen_temp=0, ref_t=0, then > I use the output from first NVT equilibration for the second input. I > repeat this to reach 300 K (in the second step nsteps=7500(*0.002=15), > gen_temp=50, ref_t=50). I 'm not sure whether this process is correct? > > Well, it works, but it's laborious and unnecessary because you're just > manually > doing what simulated annealing is doing. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > > ================================================== > -- > 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. > -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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.