[gmx-users] Temperature Annealing

[Justin Lemkul]

On 1/25/16 1:51 PM, abdus sabuj wrote:
> Hi Mark,
> I have equilibrated my system very well before the production run at 300K,
> but at time zero, the temperature is at 321K.
>
> Here is the fluctuations I am getting.
>
> time (ns)          temperature (K)
> 0                  321
> 2                  315
> 4                   333
> 6                   358
> 8                   377
> 10                 397
>

Please provide the full .mdp file, rather than just the few lines you think are 
important, as well as the commands used to continue from the previous run.  You 
probably have other incorrect settings and/or are continuing the run wrong. 
Time zero should match the previous state; the fact that it doesn't suggests 
you're not doing what you think you're doing.

-Justin

> Thanks,
> Sabuj
>
> On Mon, Jan 25, 2016 at 12:38 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> What fluctuations were you seeing over the time segments?
>>
>> Mark
>>
>> On Mon, 25 Jan 2016 19:25 abdus sabuj <sabujbuetche at gmail.com> wrote:
>>
>>> Dear gmx users,
>>>
>>> I am trying to get viscosity as a function of temperature. So I have put
>>> the following annealing inputs to the mdp file.
>>>
>>> ;simulated anneling
>>> annealing         = single
>>> annealing-npoints = 6
>>> annealing-time    = 0 2000 4000 6000 8000 10000
>>> annealing-temp    = 300 310 320 330 340 350
>>>
>>> i.e, at 10ns, the temperature should be at 350K, right? But I saw after
>> my
>>> npt simulation that, the last temperature reached at 400K. Why that's
>>> happening, did I make any mistakes?
>>>
>>> Thanks,
>>> Sabuj
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================