Subject: Temperature trouble

From: Martín Lema <[email-masked]>
Date: Mon, 24 Sep 2001 15:42:28 -0300

Dear CCLs:

In my MD simulations, I start heating up the system using Berendsen´s 
algorithm and when it reaches 300 K I switch to Andersen´s. The thing is 
the average temperature of the system then stabilizes around 294 K.

The system is a myoglobin of 2134 atoms (including hydrogens), implicitly 
solvated using the SASA algorithm and using the CHARMM27 parameter set.

I have tried different collision frequencies for the thermostat, longer 
times, longer cutoffs, etc, but I can´t find the origin of this discrepancy.

Collision values of 0 (which means no application of the thermostat) and 
166 (which means velocity is reassigned for every atom in every step) 
renders the system at 300 K, but it is not the case for more reasonable 
values in the range 0.02 - 5.
The trouble persist when performing the simulation in vacuo or using other 
solvation algorithms.

Does someone figures out where the trouble is? clues are welcome at 
[email-masked]. Useful responses will be summarized.

Martin Lema
National University of Quilmes
Argentina
.