Hi Berk! Thanks for your so fast answer! I'll try to look for a different tau_p. I would really feel 4 ps a too high value, even for water systems, but will look around before decision. Anyway, I'm still concerned about the compressibility value.
Long time ago in this list I came to this question, and this is how this ended: **>* Hi, *>* *>* Just use the water value for any liquid system (5e-5 or so). *>* *>* As the manual explains, it only affects the coupling time, not the *>* equilibrium pressure. *>* *>* Cheers, *>* *>* Erik *>*** *>* On May 3, 2006, at 8:54 PM, Jones de Andrade wrote: *>* *>* > Hi all. *>* > *>* > Ok, this may sound like a stupid question, since the equations of the *>* > barostats clearly states the compressibility constant in it. *>* > *>* > But, in other programas I used to do NpT (usually with Nosè-Hoover) *>* > simulations, like DL_Poly and MDynaMix, I never had to input this *>* > parameter. Only reference pressure and pressure coupling time were *>* > needed. *>* > *>* > Does anybody here have a clue on it? Or, in a better way to ask: how *>* > can I make an NpT simulation, of a liquid with an unknown *>* > compressibility and which I maybe would like to estimate throw *>* > simulation, preferably without running in the error of inputing this *>* > as parameter? *>* > *>* > Thanks in advance. *>* > *>* > Jones* But, what's clear from the different simulation results with different compressibilities, is that the equilibrium density changes, since different input compressibilities yelds different average box volumes. I would expect them (tau_p and compressibility) "working together" in the coupling times, but not in the average volumes or densities. That's unnexpected, and gives me a bit of trouble, since I don't like to provide the simulation with extra information from the "macroscopic world" which I can later want to extract *from* the simulation. So, how can I deal with it? And, for certanly, should the compressibility affect the simulated system's volume or not? Thanks a lot in advance! Jones On 5/3/07, Berk Hess <[EMAIL PROTECTED]> wrote:
>From: "Jones de Andrade" <[EMAIL PROTECTED]> >Reply-To: Discussion list for GROMACS users <[email protected]> >To: "Discussion list for GROMACS users" <[email protected]> >Subject: [gmx-users] Compressibility issue - real concern >Date: Thu, 3 May 2007 06:33:12 -0300 > >Hi all. > >Well, I'm having a great problem in some NpT simulations I'm running here, >which leaded me to some concerns. Let me try to explain the situation: > >Ok, I know: everywhere, including this list, amber list and any >computational chemistry list informs that the compressibility of the liquid >doesn't really matters for the NpT simulations, it will just change the >"response time" of the system. > >Knowing that, I've started to make some simulations on a new system here: >CF4. NVT equilibration, box in the proper volume, 500 molecules. After long >time, change to Parrinello-Rahman barostat. Almost blowed, but came back as >fast as almost were lost. > >I was using tau_p of 0.400 and compressibility of 116 e-6 (not even I >remember where that came from). The target volume is 45.66nm**3 at 123K and >1 atm. The potential is from AMBER, and is properly written in the topology >files (reverified that about a thousand times). > >The system kept going to a average volume around 53.4 nm**3, didn't matter >whatever I did with the simulation parameters. The reproducibility, from >the >original Kollman's paper, show's that there should be about 1-2% deviation. >I kept trying for about 1ns of simulation, couldn't be more stable (it >would >be great if it was in the correct value!). > >After all reverifications possible, I decided to change exactly what is >supposed to not alter this property: compressibility. I lowered it from >11.6e-5 to 4.5e-5. > >The volume reacted with an immediate drop to 50nm**3. > >I did not yet tried to change parrinello for berendsen. By now, I'm dealing >with the tau_p increase, from 0.400 to 0.700, which also yelded me an >reduction from 50nm**3 to 49-49.5nm**3. This means that it's not big deal >to >change the tau_p, what is also interesting since amber official and >original >guidelines uses the 0.400 ps coupling for pressure (only that with the nosè >barosthat). > >The points I'm questioning here now is: > >1 - Is the compressibility of the system a value that basically should "not >matter" what I put in there? > >2 - to what range is this "not matter" related? > >3 - I'll keep trying the compressibility, and see if will reach at some >value the expected volume. The question now is, will it reach any point >acceptable? And after this point, will it be still stable, start to grow >the >volumes again, or will just keep falling (worst scenario)? > >4 - since it should not affect the simulated property... what's happening >here, in such a way that it IS affecting the simulated property? > >I'm really sorry if this is any kind of obvious subject, but I really tried >to find any different reason for these observations. Could not find nothing >related in any list, including this one. So I thought about taking the >facts >to the discussion list and see what appears. > >Thanks in advance for anyone and any answer! > >Sincerally yours, > >Jones It's all in the manual. The compressibility beta does matter. With Berendsen the scaling formula included beta/tau, with parrinello-rahman beta/tau^2. Only these ratio matter. So changing beta changes tau. I don't know how AMBER sets the mass, but for Gromacs tau=0.4 gives oscillations with a period of 0.4 ps which is far to fast and will lead to instabilities. I would use something like tau=4 ps. Berk. _________________________________________________________________ Play online games with your friends with Messenger http://www.join.msn.com/messenger/overview _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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