Dear Amber users,
I am carrying out a NVT dynamics with shake=2 and restraints (ntr=1), I send
10 short steps of 100ps. The problem occurs when I represent energy vs time,
in a few first picoseconds the total energy does not continue with the
previous value normally but gives a big leap, each 100ps.
I solved this problem simply sending my total 1ns simulation in only one
step, but this generates large outputs.
I noticed that this problem does not appear when the dynamics not presents
shake or restraints, it seems that the two variables (ntc and ntr) are not
fully compatible ? How can I solve these first energy leaps in each 100ps
step ?
Thanks in advance,
Regards
Cristian Obiol
Biological Systems Modelling
and Drug Design Research Group
University of Barcelona
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Received on Wed Jun 08 2005 - 11:53:00 PDT
