RE: [AMBER] question of ibelly used in pmemd

From: xiaoqin huang <xqhuang1018.msn.com>
Date: Fri, 17 Jul 2009 15:36:06 +0100

thanks for your follow up, I use ntt=1, and assigned the nscm=0.



> From: ross.rosswalker.co.uk
> To: amber.ambermd.org
> Subject: RE: [AMBER] question of ibelly used in pmemd
> Date: Wed, 15 Jul 2009 18:32:07 -0700
>
> Hi Xiaoqin,
>
> As a follow up to Bob's email also make sure you set nscm=0 if you are using
> belly or restraints. Especially if you are using ntt=3.
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> > Behalf Of xiaoqin huang
> > Sent: Wednesday, July 15, 2009 2:29 PM
> > To: amber.ambermd.org
> > Subject: RE: [AMBER] question of ibelly used in pmemd
> >
> >
> > thanks for reply, and I tested:
> > 1) without nmropt=1, without ibelly=1, i.e. no restraints, no freezing,
> > just regular MD.
> > the outputs of both sander and pmemd are the same;
> > 2) with nmropt=1, but without ibelly=1, i.e. restraints, but no
> > freezing, the restrained MD.
> > the outputs of both sander and pmemd are the same;
> > 3) with nmropt=1, with ibelly=1, i.e. restraints, and freezing, do the
> > MD again,
> > when bellymask used, the error message is:
> > "ERROR: PMEMD 9 does not support bellymask option! Please use
> > Amber 6/7 GROUP format instead".
> > when the Amber 6/7 GROUP format is used, i.e. the input file I
> > attached in the previous email, the same error as described in my
> > previous email happened.
> > -------------------------------------------------------------
> > so, how to put ibelly=1 (group list or bellymask) in the input file
> > that can be read in correctly by pmemd?
> >
> >
> >
> >
> >
> > > From: rduke.email.unc.edu
> > > To: amber.ambermd.org
> > > Subject: Re: [AMBER] question of ibelly used in pmemd
> > > Date: Wed, 15 Jul 2009 14:22:23 -0400
> > >
> > > 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.msn.com>
> > > To: <amber.ambermd.org>
> > > Sent: Wednesday, July 15, 2009 1:34 PM
> > > Subject: [AMBER] question of ibelly used in pmemd
> > >
> > >
> > >
> > > Hi, users,
> > > 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!
> > >
> > > xiaoqin
> > >
> > > 09/15/2009
> > >
> >
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Received on Fri Jul 17 2009 - 10:10:09 PDT
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