Re: [AMBER] Could not read velocities from restart file

From: <>
Date: Tue, 10 Apr 2012 10:08:14 -0400 (EDT)


> restarted the computer to install some updates (first by killing the pmemd
> process, which may not have been the proper way).

I would agree that this is not the proper way and that one should split
long simulations into pieces and keep intermediate rst-files (check the
ntwr<0 option) so that precisely this does not happen, but anyways:

> Upon restarting the simulation, I get the error at the bottom of the new
> output file:
> | ERROR: Could not read velocities from 4.rst

Check if your rst file contains the correct 3*N number of coordinates and
3*N velocities. If you were unlucky enough to kill the process right when
it was halfway done with writing a rst file, you may have truncated and
thereby corrupted it.

However all is not lost I guess:

if your rst file contains enough coordinates (3*natom, so natom/2+3 lines)
and only misses velocities, you could delete all velocity lines and just
restart your system (ntx=1) at 300K. This introduces a little disturbance
but that should rapidly equilibrate away (in few ps). You may have to rest
the box in xleap, as box coordinates are at the end of the rst-file.

If your rst file is unusable, you could extract the last snapshot from the
mdcrd-file and convert it into a rst (via ptraj) and restart your
simulation from that point. crd-files have a lower accuracy than
rst-files, but again, this should equilibrate away very quickly, compared
to a multinanosecond simulation.

if ptraj cannot read your crd file either, you can (if you used ASCII
mdcrd format) parse through the mdcrd by yourself and see if you can
extract a useful snapshot as far advanced in your trajectory as possible
and restart from there.

Each of these solutions would introduce a small but in my opinion
acceptable inaccuracy into your system. That may be difficult to explain
in a paper, but otherwise you should be ok.

For materials and methods: ;-)

"At 1448 ns simulation time, velocities were discarded and replaced by a
Boltzmann velocity distribution at room temerature. This procedure was
conducted to ensure proper system equilibration and stability. (innocent



Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

AMBER mailing list
Received on Tue Apr 10 2012 - 07:30:04 PDT
Custom Search