[AMBER] temp ramping in tutorial A5

From: Robert Wohlhueter <bobwohlhueter.earthlink.net>
Date: Mon, 30 Mar 2015 18:33:31 -0400

Working my way through Advanced tutorial A5 (NEB) on a standalone,
4-processor, AMD-64 machine, running Amber14, under Ubuntu 14.04.

In section 4, "heating up", I run into the following problem. Though
everything appears to run alright under sander.MPI, in fact, inspection
of the "-.out" files, any and all, shows that the temperature is
remaining at 0 degK. I've checked and rechecked the syntax, especially
the $wt namespace (&wt type='TEMP0', istep1=0,istep2=35000,value1=0.0,
value2=300.0). Similar syntax, e.g. in the B0 tutorial ("02_Heat.in"}
has worked fine..

One additional disclosure, which might be at fault (if it is, then I
really don't comprehend what's going on in NEB!) Because I have only 4
processors (so, mpirun -np 4), I can't use "-ng 32", so I have broken up
the tutorial's "groupfile" into 8 subgroup files, each comprising 4
lines of the original groupfile. Is that kosher? Is there some reason
this piecemeal approach might interfere with the replicate communication
in a way that might prevent temperature ramping?

Any nudges will be appreciated,

Bob Wohlhueter

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Received on Mon Mar 30 2015 - 16:00:02 PDT
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