[gmx-users] Compressibility issue - real concern

Jones de Andrade johannesrs at gmail.com
Thu May 3 12:37:07 CEST 2007

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

**>* 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!


On 5/3/07, Berk Hess <gmx3 at hotmail.com> wrote:
> >From: "Jones de Andrade" <johannesrs at gmail.com>
> >Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> >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.
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