AMBER Archive (2003)

Subject: Re: AMBER: pmemd

From: james tomomi macdonald (j.macdonald_at_mail.cryst.bbk.ac.uk)
Date: Mon Aug 18 2003 - 11:05:20 CDT

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 pmemd
> > 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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