[gmx-users] heating

[rajat desikan]

Hi Kiana,
Simulated annealing will take your system temperature distribution to the
target temperature. So, I always start at the starting point.

Hi Vitaly,
Heating slowly (over many ns) from 0K-xK seems to be an important step in
crystal simulations performed by other members in my lab...in fact, many
such heating and cooling cycles are performed before a production run...the
relevance to biomolecular systems may be debatable.


On Wed, Dec 4, 2013 at 4:57 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>wrote:

> Honestly, I see no sense in heating from from 0 to 300 K. As long as
> the system is in the solid state, it is probably not informative to
> handle it. Thus heating, if any, might start from the freezing point.
> Moreover, heating from 0 to 300 K over 100 ps is so fulminant that it
> does not correspond to any real process...
>
>
> Dr. Vitaly V. Chaban
>
>
> On Wed, Dec 4, 2013 at 8:58 AM, rajat desikan <rajatdesikan at gmail.com>
> wrote:
> > 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
> > --
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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