AMBER Archive (2009)
Subject: [AMBER] question of ibelly used in pmemd
From: xiaoqin huang (xqhuang1018_at_msn.com)
Date: Wed Jul 15 2009 - 12:34:20 CDT
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. there
> are certainly many other papers that are relevant, so make sure to check out
> 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 <case_at_biomaps.rutgers.edu>wrote:
> > 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
> AMBER mailing list
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