[gmx-users] Re: energy conservation / frozen atoms
jalemkul at vt.edu
Sat Aug 3 03:49:00 CEST 2013
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 A. Lemkul, Ph.D.
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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