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. I hope this will be helpful from the development standpoint. Regards, Alireza >> > >> ------------------------------ > >> > >> Message: 3 > >> Date: Tue, 30 Jul 2013 07:20:53 -0400 > >> From: Justin Lemkul <jalem...@vt.edu> > >> Subject: Re: [gmx-users] energy conservation / frozen atoms > >> To: Discussion list for GROMACS users <gmx-users@gromacs.org> > >> Message-ID: <51f7a195.80...@vt.edu> > >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed > >> > >> > >> > >> On 7/29/13 10:51 PM, S. Alireza Bagherzadeh wrote: > >>> Hi All, > >>> > >>> I am simulating a system in which I have two solid surfaces and I keep > >> them > >>> frozen during simulations. I also exclude the interactions between its > >>> atoms to avoid spurious contribution to the virial pressure due to > large > >>> forces between them as suggested in the manual. > >>> > >>> I run a nvt for equilibration and then I do the production run in an > nve > >>> ensemble; however, I am not getting good energy conservation. There is > a > >>> huge energy drift... > >>> > >>> > >>> When I remove the solid surfaces, I will only have water molecules and > >>> united atom methane molecules in my system. Using the same protocol I > >>> obtain a very good energy conservation... > >>> > >> > >> What happens if you unfreeze the frozen surfaces and run the same > system? > >> > > > > The point is I do not want to do this as I am trying to save some > > calculations. > > My point in asking is to do some diagnostics. There are countless similar > posts > to yours - freeze some group(s), energy conservation is bad, and then a > dead end > to the thread. It would be interesting, from a development standpoint, to > know > whether the issue is truly linked to the frozen group(s). Using strong > position > restraints in lieu of frozen groups is probably a reasonable workaround > that > could also be used to find a problem. > > > My system is already big and including all of the bond, angles and > dihedral > > interactions of the solid surfaces slows down the simulation > considerably. > > > > The bonded interactions are not likely what slows the system down. > Freezing > doesn't actually improve performance. Using energygrp_excl is what causes > a > speed-up. > > > > > > >> > >>> Any insight on what might be wrong in my system would be very > >> appreciated. > >>> > >> > >> The contents of the .edr file will probably be informative, as you can > >> identify > >> which energy term(s) is(are) most affected. It's all probably related > to > >> the > >> frozen surfaces themselves acting as an energy sink or something. > >> > > > > Is there anyway to fix the "energy sinking" effect of the surfaces? > > That's just an off-the-cuff guess at something being wrong. Like I said > above, > there's been no thorough evaluation of whether or not this sort of > combination > does (or should) work. > > > I used dl_poly to simulate a similar system and there was no problem with > > the energy conservation. > > > > That's been reported before, hence something is probably wrong with > Gromacs, but > we need more information to figure it out and fix it. Otherwise, you'll > have to > figure out an alternate strategy. > > -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 > > ================================================== > > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
