[AMBER] Assigning new velocities from Maxwell-Boltzmann distribution (ntx = 1)

From: German P. Barletta <pbarletta.gmail.com>
Date: Sun, 9 Aug 2020 17:43:20 -0300

Dear Amber users,
     I'm trying to enhance sampling by taking frames of interest from a run
and assigning them new velocities to start new replica runs (poor man's
adaptive sampling).

     When I start new replicas, I give them 5ns for "re-equilbration". The
input for this re-equilibration is the same as the one for production but
instead of reading velocities from the input file (ntx = 5), I assign new
velocities at random (ntx = 1).

      The problem is, for some reason, Amber says the starting temperature
(~450K) is way higher than it is supposed to be (temp0 = tempi = 300.0) .
100ps after, it's back to normal.

Should I be worried? This happens with every replica I run. I'm attaching
an output files from one of the replicas.

I'd be thankful for any help.

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Received on Sun Aug 09 2020 - 14:00:02 PDT
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