AMBER Archive (2009)

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

From: xiaoqin huang (xqhuang1018_at_msn.com)
Date: Fri Jul 17 2009 - 09:54:55 CDT

thanks, but I still have question about pmemd run
here I attached again the modified input and output of pmemd (amber 9), please help me to figure out what is wrong over there.
>From the output file, I found that the ibelly groups were read in, and the MD got started, but still something is wrong over there when compare the energy terms of the first step in output file with those in the output of sander runs for the same system.
and after several steps, it stoped.

so even the ibeely group was read in, but I donot know how it was parsed.

> 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 17:56:00 -0400
>
> You have to use the group format like it says. I believe you need to put the
> nmr redirection stuff after the last namelist, and then list your belly
> restraints. The *.in you gave in your earlier mail does not look correct to
> me, in that the group input does not start with a comment card; you may have
> to look at the doc on GROUP input again.
> Regards - Bob Duke
> ----- Original Message -----
> From: "xiaoqin huang" <xqhuang1018_at_msn.com>
> To: <amber_at_ambermd.org>
> Sent: Wednesday, July 15, 2009 5:28 PM
> 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 Hotmail®.
> http://windowslive.com/Tutorial/Hotmail/QuickAdd?ocid=TXT_TAGLM_WL_HM_Tutorial_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

_________________________________________________________________
Windows Live™: Keep your life in sync.
http://windowslive.com/explore?ocid=TXT_TAGLM_WL_BR_life_in_synch_062009

  • application/octet-stream attachment: tus1.in

  • application/octet-stream attachment: tus1.out


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