rajatdesikan at gmail.com
Wed Dec 4 08:59:10 CET 2013
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
On Wed, Dec 4, 2013 at 12:18 PM, kiana moghaddam <ki_moghaddam at 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 <jalemkul at vt.edu>
> 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
> the system is likely not going to be stable or effective because the
> will go haywire trying to compensate for such a drastic change in
> 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
> 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
> doing what simulated annealing is doing.
> 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
> jalemkul at 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
> * 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-request at gromacs.org.
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
More information about the gromacs.org_gmx-users