Re: [AMBER] Output format in sander

From: Jason Swails <>
Date: Wed, 01 Jul 2015 11:55:59 -0400

On Wed, 2015-07-01 at 00:38 -0400, Brent Krueger wrote:
> And to add to this...
> If one looks at the format statements that go along with the code John
> showed in his original email, it seems clear to me that these statements in
> the dynlib.F90 do not represent what is in the mden file.
> But maybe it is easier to come back to his original question. If one
> wanted to modify the format of the mdout file. Where is the code that
> actually writes this?

I was able to go back and look more carefully at the original post and
the sander source code. This *is* the correct place to modify the code
(and unit 6 *is* the mdout file). If changes to this subroutine are not
reflected in the mdout (unit 6) or mdinfo (unit 7), then this almost
certainly means that the new sander that's getting built is *not* the
same sander that is being used for the calculations. Which means the
best way to debug this is to try and find out why this might be
happening. Time stamps help here. Some possibilities:

1. You have configured and installed in parallel, but are using the
serial "sander" executable.
2. The opposite (you have configured and installed in serial, but are
using the "sander.MPI" executable)
3. You have a separate Amber installation that is unknowingly being used
for the simulations that is not the same copy as the one being modified

It's impossible to tell for sure, but John *is* modifying the correct
file in the correct place to adjust the output formatting in the mdinfo
and mdout (he has to make those changes in both the write(6 and write(7
locations to make the format changes in both the mdout and mdinfo,


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Jul 01 2015 - 09:00:02 PDT
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