Re: [AMBER] question of ibelly used in pmemd

From: Robert Duke <>
Date: Wed, 15 Jul 2009 22:56:00 +0100

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" <>
To: <>
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
     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:
> To:
> 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" <>
> To: <>
> 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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