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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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