[gmx-users] heating

[Dr. Vitaly Chaban]

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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