Re: [AMBER] TI in vacuum

From: <>
Date: Wed, 2 Feb 2011 04:17:29 -0500 (EST)


well the pdb look fine but doesnt help much.

>>> > In the second transformation, it stops at lambda=0.1, and the v0
>>> stops
>>> > with
>>> > no error message and v1 terminates normally, again.

hm, one process dying and the other running to completion? That should not
be possible, since each process requires info from the other to advance.
This makes it sound like a problem of running sander as opposed to a
problem with the chemical model. Does the same thing occur on different
machines? If you use just two CPUs without a queueing system? If you
slightly change lambda?

>>> > I am not writing a trajectory file for each lambda. For each lambda,
>>> i
>>> am
>>> > just writing a coordinate file that corresponds to the last
>>> structure.

Try and run one that you know will fail and write out the trajectories
each step, then compare V0 and V1 for e.g. coordinate mismatches.


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

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Received on Wed Feb 02 2011 - 01:30:02 PST
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