AMBER Archive (2009)

Subject: Re: [AMBER] temperature rises with igb=1

From: David A. Case (
Date: Thu Mar 19 2009 - 07:04:54 CDT

On Thu, Mar 19, 2009, Bala subramanian wrote:

> 1) The plot of temp Vs time (a.pdf) shows that, when i use ntt=3 and
> gamma_ln =1, the fluctuation in temperature goes down as i reduce the
> restraint from 25 to 5 to 0.

This indicates that the combination of a strong restraint force (25 or
5) plus a weak thermostat (gamma_ln=1) gives you fluctuations in
temperature, which are not themselves bad. Do you really need to have
restraints (after some short intial equilibration)? If so, try reducing
the restraint weight (say to 1 or 0.5 or 0.1) and increasing gamma_ln to
something like 5.

In spite of the fact that the *average* temperature looks good with
ntt=1, you don't get much effective thermalization in implicit solvent,
and you can easily get persistent hot- or cold-spots in a simulation.

It doesn't look like you are doing anything wrong, but are rather
exploring parameter ranges that people don't often use.


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