AMBER Archive (2003)

Subject: Re: AMBER: pmemd

From: Robert Duke (rduke_at_email.unc.edu)
Date: Mon Aug 18 2003 - 11:51:16 CDT

James -
Looks like possibly some higher energy stuff, but I would also note that it
would be worthwhile trying to set iwrap=1. I quote from the amber 7 manual:
"For very long runs, setting iwrap=1 may be required to keep the coordinate
output from overflowing the trajectory file format". Using COM keeps the
center of mass at the center of the box. In long runs (or probably shorter
runs with higher velocities), you will still see the atoms spreading out in
space unless wrapping is done. I would suspect a problem with the
simulation unless it is very long, and actually, I am suspicious of the high
COM velocity being removed (I typically see 0 here, but I spend more time
writing code than doing simulations). I would be interested in a
comparable sander 7 run, but with IDENTICAL run conditions, starting with a
well minimized structure. The fact someone else is doing a run on another
system with sander 7 without problems means nothing (we actually have a heck
of a lot on nsec accumulated with pmemd running on big protein simulations
with no problems in our group). And by the way, sander 7 may be broken
under mpi for minimizations (problem recently reported to Prof. Case) - it
gives different results fairly quickly when run with mpi as opposed to a
uniprocessor version - so I currently don't trust sander 7 for mpi
minimizations (I still use 6, or pmemd which agree in all implementations).
Anyway, I would be interested in your starting files just out of
minimization, the files right before the system goes south, and the "gone
south" files. I also think it would be valuable for some of the real MD
pros to speak up on this one. I am more of a software guy.
Regards - Bob

----- Original Message -----
From: "james tomomi macdonald" <j.macdonald_at_mail.cryst.bbk.ac.uk>
To: <amber_at_scripps.edu>
Sent: Monday, August 18, 2003 12:05 PM
Subject: Re: AMBER: pmemd

>
> Hi Bob,
>
> Actually, having looked at it further, it appears that there has been
> quite a high COM velocity during my simulation (which is being removed),
> and some of the coordinates have gone over -999, so a couple of
> lines read:
>
> -207.0612654-164.0880036-682.2872437-521.2708399-275.5480435************
> -521.3560550-275.9826974************-521.9206418-275.9782509************
>
> for example this is a typical line from my output file:
>
> check COM velocity, temp: 0.018330 0.51(Removed)
>
> I haven't tried running it on sander 7, but i am thinking of trying to see
> if i still get high COM velocities.
>
> I think the solution would be to subtract a constant value from all the
> coordinates.
>
> A work mate has been running other simulations with almost identical input
> parameters on a different protein on sander 7, but is not getting high COM
> velocities.
>
> If you would still like to have a look at my files, then i would be happy
> to email them to you.
>
> Thanks for your help,
> Cheers,
>
> James.
>
>
> On Mon, 18 Aug 2003, Robert Duke wrote:
>
> > Date: Mon, 18 Aug 2003 11:45:47 -0400
> > From: Robert Duke <rduke_at_email.unc.edu>
> > Reply-To: amber_at_scripps.edu
> > To: amber_at_scripps.edu
> > Subject: Re: AMBER: pmemd
> >
> > James -
> > Have you tried to read it in either sander 6 or 7 (depending on which
mode
> > you are running pmemd in)? It could just be a corrupted file. If you
wish,
> > feel free to make a gzipped tarball of the various files needed to repro
the
> > problem, and I'll take a look. I would bet on a truncated or otherwise
> > corrupted restrt, though (what happens if you redo the run that creates
the
> > restart - do you get exactly the same thing; is there any platform
mixing
> > with binary files?)
> > Regards - Bob Duke
> > ----- Original Message -----
> > From: "james tomomi macdonald" <j.macdonald_at_mail.cryst.bbk.ac.uk>
> > To: <amber_at_scripps.edu>
> > Sent: Monday, August 18, 2003 11:18 AM
> > Subject: AMBER: pmemd
> >
> >
> > >
> > > Hi,
> > >
> > > I am having a peculiar problem with pmemd. I have been able to run pm
emd
> > > with no problem for a few weeks, but i have recently got a problem i
can't
> > > understand. For some reason it has become unable to read my restart
> > > coordinate file reporting the error:
> > >
> > > FATAL: Could not read coords from production_105.xyz
> > >
> > > I have looked at the file production_105.xyz manually (and it looked
OK)
> > > and tried regenerating it to see if there was some kind of one-off
error
> > > when it was written.
> > >
> > > I would be very grateful if anyone could help me, and i could forward
on
> > > the file should that be necessary.
> > >
> > > Thanks very much in advance.
> > >
> > > James.
> > >
> > >
> > >
> >
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