AMBER Archive (2009)
Subject: Re: [AMBER] question of ibelly used in pmemd
From: Robert Duke (rduke_at_email.unc.edu)
Date: Wed Jul 15 2009 - 13:22:23 CDT
If you take the exact same system, run it in sander, and run it in pmemd, it
should do the exact same thing for about 300-500 steps; then the systems
will diverge due to rounding errors in the algorithms (which is of no
concern - just different regions in phase space). So, is this what you are
doing? If so, then it is likely their is some software installation problem
or hardware problem. Did pmemd pass the amber test suite on your machine?
It should. Okay, all that said, I looked at your mdin, and you have a
pretty complex setup, involving both belly and nmr restraints. There is
some possibility this is not being parsed exactly correctly in pmemd, but I
think it is probably okay (I hardly ever use nmr restraints, so someone more
familiar may want to look at how that is being used here). Looking at the
output, what I see primarily is that the run goes for over 10 steps, but
then there is an end-of-file on the restrt file; I am wondering if you had a
hardware issue of some sort here... I would retry with both sander and
pmemd, but for 10 steps, dumping output with each step (ntpr = 1), and see
if there are any differences between pmemd and sander.
Regards - Bob Duke
----- Original Message -----
From: "xiaoqin huang" <xqhuang1018_at_msn.com>
Sent: Wednesday, July 15, 2009 1:34 PM
Subject: [AMBER] question of ibelly used in pmemd
I have a question about ibelly=1 used in pmemd simulations.
the situation is that I want to freeze some part of residues/atoms of the
system, so I used the ibelly=1 in the sander, it works well no matter which
version (8, 9, 10).
when I used the same ibelly=1 in the pmemd (amber 9), the MD runs and then
stopped with the message as vlimit exceeded for step 1...
here attached is the input file, output file and the error message.
any suggestions or comments? thanks!
Subject: RE: [AMBER] ask for parm99MOD
Date: Mon, 1 Jun 2009 16:25:02 -0400
thanks, I am reading a lot of papers on force fields from Giants like you
and others. Later on, I think I will have a rough idea of how to choose an
appropriate force field in Amber for my studying system.
> From: carlos.simmerling_at_gmail.com
> Date: Mon, 1 Jun 2009 16:12:47 -0400
> Subject: Re: [AMBER] ask for parm99MOD
> To: amber_at_ambermd.org
> sorry for the slow follow-up. here's another reference from my group.
> are certainly many other papers that are relevant, so make sure to check
> some of the ones we cite as well
> **Okur, A., Wickstrom, L. and Simmerling, C.,* “Evaluation of salt bridge
> structure and energetics in peptides using explicit, implicit and hybrid
> solvation models”*, J. Chem. Theory Comput., 4:288-298 (2008)
> On Thu, May 28, 2009 at 5:52 PM, David A. Case
> > On Thu, May 28, 2009, Carlos Simmerling wrote:
> > > unless you have a reason to think about ff02, don't involve it any
> > > more.
> > Just my two cents here: Unless you are explicitly trying to reproduce
> > some
> > old result, we advise that people only use force fields in
> > $AMBERHOME/dat/leap/cmd, and *not* those in the "oldff" subdirectory,
> > which
> > are only there for historical completeness.
> > The ff02 model has undergone some amount of torsional
> > reparameterization,
> > as
> > discussed in Wang et al, (2006) JCC, 27(6), 781-790. However, this is a
> > polarizable force field, and hence is not compatible with any of Amber
> > GB
> > models. You could use leaprc.ff02pol.r1 ("r1" = revision 1) for
> > explicit
> > solvent simulations, but not for GB.
> > > if you just want to run the best simulation that you can, I suggest
> > ff99SB
> > > (but be careful with GB, the GB-OBC model is very good but does have a
> > few
> > > minor weaknesses that have also been reported in the literature).
> > Just to expand, be sure to read this paper:
> > %A D.R. Roe
> > %A A. Okur
> > %A L. Wickstrom
> > %A V. Hornak
> > %A C. Simmerling
> > %T Secondary Structure Bias in Generalized Born Solvent Models:
> > Comparison
> > of
> > Conformational Ensembles and Free Energy of Solvent Polarization from
> > Explicit
> > and Implicit Solvation
> > %J J. Phys. Chem. B
> > %V 111
> > %P 1846-1857
> > %D 2007
> > (Carlos can chime in if there are others as well).
> > ...dac
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
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