[gmx-users] heating

[rajat desikan]

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_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>
> 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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
>
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-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore