[gmx-users] Re: energy conservation / frozen atoms

[Justin Lemkul]

On 8/2/13 3:19 PM, S. Alireza Bagherzadeh wrote:
> Thanks for your notes.
>
>
> I did a diagnosis test which could be of relevance here.
>
> I set up the following system:
> [ gas | liquid water (solid water) liquid water | gas ]
>
> gas is united atom methane.
> liquid water is tip4p-ice model and solid water is a cage-like crystalline
> structure of water and methane called gas hydrate.
>
> Now, in order to test the effect of freezing and position restraining on
> the performance of nve I did two tests at 370 K.
>
> Test 1 (freezing):
> Solid water was kept frozen in all 3 dimensions (Y Y Y).
> First I ran a nvt for 250 ps for equilibration (potential and total energy
> both converged after 250 ps, Pressure equilibrated at ~ 3950 bar). Then I
> started a 1ns nve.
> Similar to my other simulation, the total energy linearly decreased (0.84%
> per ns) as well as potential energy. Pressure remained around 3950 bar;
> however, the temperature decreased from 370 to 364 K (physically, this
> should not happen).
>
>
> Test 2 (position restraining):
> Oxygen of solid water was strongly restrained to a point (fc of 100000).
> Similar to the previous test, first I ran a nvt for 250 ps for
> equilibration (potential and total energy both converged after 250 ps,
> Pressure equilibrated at about 0 bar with fluctuations of ~ 2000 bar). Then
> I started a 1ns nve.
> Again, similar to test 1, the total energy linearly decreased (1.33% per
> ns) as well as potential energy. Pressure remain around 0 bar; however, the
> temperature initially dropped from 370 K to 355K within 1 ps, then
> increased to 358 K during the next 50 ps and thereafter kept linearly
> decreasing to 353 K until the end of 1 ns run (physically and intuitively,
> this should not happen).
>
>
>
> (In  both of the tests, I kept the methane inside the cages of solid water
> position-restrained to a point by fc = 1000).
>
> If needed I can post the .mdp and .top files too.
>

An .mdp file would be useful, otherwise a demonstration that these parameters 
actually produce an energy-conserving NVE ensemble for a simple system.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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