Hi Berk! Thanks for your so fast answer!<br><br>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.
<br><br>Long time ago in this list I came to this question, and this is how this ended:<br><br><pre><i></i>><i> Hi,<br></i>><i><br></i>><i> Just use the water value for any liquid system (5e-5 or so).<br></i>>
<i><br></i>><i> As the manual explains, it only affects the coupling time, not the<br></i>><i> equilibrium pressure.<br></i>><i><br></i>><i> Cheers,<br></i>><i><br></i>><i> Erik<br></i>><i></i><i><br>
</i>><i> On May 3, 2006, at 8:54 PM, Jones de Andrade wrote:<br></i>><i><br></i>><i> > Hi all.<br></i>><i> ><br></i>><i> > Ok, this may sound like a stupid question, since the equations of the<br></i>
><i> > barostats clearly states the compressibility constant in it.<br></i>><i> ><br></i>><i> > But, in other programas I used to do NpT (usually with Nosè-Hoover)<br></i>><i> > simulations, like DL_Poly and MDynaMix, I never had to input this
<br></i>><i> > parameter. Only reference pressure and pressure coupling time were<br></i>><i> > needed.<br></i>><i> ><br></i>><i> > Does anybody here have a clue on it? Or, in a better way to ask: how
<br></i>><i> > can I make an NpT simulation, of a liquid with an unknown<br></i>><i> > compressibility and which I maybe would like to estimate throw<br></i>><i> > simulation, preferably without running in the error of inputing this
<br></i>><i> > as parameter?<br></i>><i> ><br></i>><i> > Thanks in advance.<br></i>><i> ><br></i>><i> > Jones</i></pre><br>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.
<br><br>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.
<br><br>So, how can I deal with it? And, for certanly, should the compressibility affect the simulated system's volume or not?<br><br>Thanks a lot in advance!<br><br>Jones<br><br><div><span class="gmail_quote">On 5/3/07,
<b class="gmail_sendername">Berk Hess</b> <<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br><br><br>>From: "Jones de Andrade" <<a href="mailto:johannesrs@gmail.com">johannesrs@gmail.com</a>><br>>Reply-To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org
</a>><br>>To: "Discussion list for GROMACS users" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>>Subject: [gmx-users] Compressibility issue - real concern<br>>Date: Thu, 3 May 2007 06:33:12 -0300
<br>><br>>Hi all.<br>><br>>Well, I'm having a great problem in some NpT simulations I'm running here,<br>>which leaded me to some concerns. Let me try to explain the situation:<br>><br>>Ok, I know: everywhere, including this list, amber list and any
<br>>computational chemistry list informs that the compressibility of the liquid<br>>doesn't really matters for the NpT simulations, it will just change the<br>>"response time" of the system.<br>>
<br>>Knowing that, I've started to make some simulations on a new system here:<br>>CF4. NVT equilibration, box in the proper volume, 500 molecules. After long<br>>time, change to Parrinello-Rahman barostat. Almost blowed, but came back as
<br>>fast as almost were lost.<br>><br>>I was using tau_p of 0.400 and compressibility of 116 e-6 (not even I<br>>remember where that came from). The target volume is 45.66nm**3 at 123K and<br>>1 atm. The potential is from AMBER, and is properly written in the topology
<br>>files (reverified that about a thousand times).<br>><br>>The system kept going to a average volume around 53.4 nm**3, didn't matter<br>>whatever I did with the simulation parameters. The reproducibility, from
<br>>the<br>>original Kollman's paper, show's that there should be about 1-2% deviation.<br>>I kept trying for about 1ns of simulation, couldn't be more stable (it<br>>would<br>>be great if it was in the correct value!).
<br>><br>>After all reverifications possible, I decided to change exactly what is<br>>supposed to not alter this property: compressibility. I lowered it from<br>>11.6e-5 to 4.5e-5.<br>><br>>The volume reacted with an immediate drop to 50nm**3.
<br>><br>>I did not yet tried to change parrinello for berendsen. By now, I'm dealing<br>>with the tau_p increase, from 0.400 to 0.700, which also yelded me an<br>>reduction from 50nm**3 to 49-49.5nm**3. This means that it's not big deal
<br>>to<br>>change the tau_p, what is also interesting since amber official and<br>>original<br>>guidelines uses the 0.400 ps coupling for pressure (only that with the nosè<br>>barosthat).<br>><br>>The points I'm questioning here now is:
<br>><br>>1 - Is the compressibility of the system a value that basically should "not<br>>matter" what I put in there?<br>><br>>2 - to what range is this "not matter" related?<br>><br>
>3 - I'll keep trying the compressibility, and see if will reach at some<br>>value the expected volume. The question now is, will it reach any point<br>>acceptable? And after this point, will it be still stable, start to grow
<br>>the<br>>volumes again, or will just keep falling (worst scenario)?<br>><br>>4 - since it should not affect the simulated property... what's happening<br>>here, in such a way that it IS affecting the simulated property?
<br>><br>>I'm really sorry if this is any kind of obvious subject, but I really tried<br>>to find any different reason for these observations. Could not find nothing<br>>related in any list, including this one. So I thought about taking the
<br>>facts<br>>to the discussion list and see what appears.<br>><br>>Thanks in advance for anyone and any answer!<br>><br>>Sincerally yours,<br>><br>>Jones<br><br>It's all in the manual.<br><br>
The compressibility beta does matter.<br>With Berendsen the scaling formula included beta/tau,<br>with parrinello-rahman beta/tau^2.<br>Only these ratio matter.<br>So changing beta changes tau.<br><br>I don't know how AMBER sets the mass, but for Gromacs tau=
0.4<br>gives oscillations with a period of 0.4 ps which is far to fast<br>and will lead to instabilities. I would use something like tau=4 ps.<br><br>Berk.<br><br>_________________________________________________________________
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