AMBER Archive (2009)

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

From: Robert Duke (
Date: Fri Jul 17 2009 - 10:48:41 CDT

Okay, there is an &end on line 23 of that I believe is unnecessary,
but I don't think it is causing any problems. However I notice that the last
entry in your "belly group" residue listing, on line 49, specifies residues
533-150000. That happens to be roughly 49,000 more residues than your
system has... (the NRES printed out in your mdout says your system has
100,441 residues and 308,147 atoms). I would suspect that the group reading
code in pmemd as well as sander may have a bit of trouble with this, though
maybe I am wrong (well I looked, and it seems the code can, at least on a
quick read, reset any excessive residue numbers to nres; I would still not
do this) Another point, you specify a cutoff of 15 in your mdin for an ewald
run. This should work, but has no benefit whatsoever. In fact, you are
probably running about six times slower than you really need to because of
this large cutoff, and consuming 6x as much memory in the pairlists. The
whole idea of particle mesh ewald, the default electrostatics method in
pmemd or sander, is to combine a small direct space calc (ie., a short
default direct space cutoff) with a reciprocal space calc on the rest of the
unit cell in order to get an electrostatics calc fully representing the
system with no effective cutoff, accurate to 4-5 decimal places, and more
efficient (and accurate) than a pure cutoff system with a longer cutoff.
Here, specifying a 15 angstrom cutoff, you are pretty much shooting yourself
in the foot and wasting computer time. If you want better vdw numbers than
provided by the 8 angstrom default, you can specify a longer cutoff of say 9
angstroms; that combined with the default analytic vdw correction (vdwmeth
1) will give you reasonable accuracy for your vdw numbers. So looking at
the output, you start hot (~444K) and quickly are heating further, I really
don't know what may be wrong with the system, and would have to do a bunch
more work with the whole system to know whether what you are experiencing is
caused by a bad system, bad input, or a bug. Once again, what happens with
sander? The output on group reads, nmr redirs, etc. looks like everything
was read fine in pmemd, but I really can't be sure based on the info I have.
I would try the smaller cutoff (just remove cut = 15 and you will default to
8) on a whim; it will greatly reduce your memory usage, and if you are
running this on 8 cpu's in one box with limited memory (it is a big system),
that could help. But I still think that given that you start at 444K for a
temp, you may have a basic system problem here, that will have to be fixed
by starting over and very carefully considering what you are doing.
- Bob Duke
----- Original Message -----
From: "xiaoqin huang" <>
To: <>
Sent: Friday, July 17, 2009 10:54 AM
Subject: RE: [AMBER] question of ibelly used in pmemd

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