From: "Jones de Andrade" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: "Discussion list for GROMACS users" <gmx-users@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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