Re: [AMBER-Developers] Trajectory Writes During Xmin

From: <>
Date: Tue, 07 Aug 2012 20:24:08 +0200

Hi Dan,

XMIN and LMOD know nothing about trajectories and IMHO they shouldn't.
  They both read input coordinates and provide output coordinates; it
is entirely up to the calling program to decide what to do with these
coordinates. Of course I mean the core XMIN and LMOD libraries, the
top level wrappers are part of Amber and that would be the place to
implement any of your options. As for the LMOD tests, they are
expected to be different on different architectures, etc., in terms of
the few steps these tests involve, but they should look qualitatively
similar, which of course is difficult to do with diff. I believe we
have a comment regarding this in the test.lmod output.


Quoting Daniel Roe <>:

> Hi All,
> There are a few issues in the code concerning trajectory writes during
> Xmin. Current behavior is that at least the first and last frames of a
> trajectory are always written irrespective of the ntwx flag. However,
> in the code the trajectory file is not opened when ntwx is 0, so when
> running lmod with ntwx=0 the trajectory file is always written to
> 'fort.12' if ioutfm=0 and a NetCDF error occurs if ioutfm=1. Should 1)
> xmin pay attention to the ntwx flag (that is, no trajectory write if
> set to 0), 2) should open_dump_files know about lmod, or 3) should
> lmod make its own amopen calls? My vote is for option 1 since that is
> the behavior most users would expect.
> -Dan
> PS - The test.lmod tests all fail - is this expected? (they aren't
> being run anymore by default)
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> (801) 587-9652
> (801) 585-9119 (Fax)
> _______________________________________________
> AMBER-Developers mailing list

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Received on Tue Aug 07 2012 - 11:30:03 PDT
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