AMBER Archive (2009)

Subject: RE: [AMBER] question of ibelly used in pmemd

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Jul 15 2009 - 20:32:07 CDT

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_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of xiaoqin huang
> Sent: Wednesday, July 15, 2009 2:29 PM
> To: amber_at_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_at_email.unc.edu
> > To: amber_at_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_at_msn.com>
> > To: <amber_at_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
> >
>
> _________________________________________________________________
> Insert movie times and more without leaving HotmailR.
> http://windowslive.com/Tutorial/Hotmail/QuickAdd?ocid=TXT_TAGLM_WL_HM_T
> utorial_QuickAdd_062009_______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber