AMBER Archive (2005)

Subject: AMBER: total energy leaps

From: cristian obiol (c.obiol_at_qf.ub.es)
Date: Wed Jun 08 2005 - 05:44:18 CDT

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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