Subject: Equilibration stage in MD simulations

From: Didier MATHIEU <[email-masked]>
Date: Wed, 18 Mar 1998 07:02:11 +0000

Dear all, 

While involved so far mostly in estimating organic materials properties
from the features of
isolated molecules, I consider now carrying out condensed matter
simulations in periodic boxes.,
for solids and liquids as well. 
However, with regard to non-microcanonic molecular dynamics simulations,
some procedures
used for equilibration are unclear to me. 

For instance, in J. Phys. Chem. B 101, 798-808 (1997) Sorescu, Rice and
Thompson did
simulations of a molecular crystal in 3 stages, which are, according to
my understanding of the
paper : 
   1. NVT simulation (4 ps) 
   2. NVE simulation (6 ps) 
   3. NPT simulation (10 ps) for each T, at P=0 with velocities scaling
for the first 4 ps and
averages    recording for the 6 last ps. 

Were I to record averages in the NPT ensemble, I would naively have
first equilibrated the system
through NPT simulations, then I would have computed NVE trajectories to
estimate averages. 
I think I need some advice to understand how to perform non-NVE
simulations. 

Here are related questions : 
* In the abovementionned paper, averages are recordes from NPT
trajectories, without velocities
scaling. Therefore, how is temperature constrained ? No mention is made
in the paper of any
thermostat such as Nose's. 
* On the other hand, it is not clear to me whether it is meaningful to
record averages when the
equations of motion are not strictly Newton's, i.e. not in the
microcanonical ensemble. For
instance in the NVT ensemble it is intuitive that the average could in
principle be obtained over a
set of NVE trajectories with the energy E sampled in the canonical
ensemble according to the
temperature T. However, it is not so clear whether it is meaningful to
record averages from
trajectories derived from Nose's equations, for instance... 
Thanks to anybody which could enlight me on these subjects. 
Regards 

-- 
Didier MATHIEU
CEA - Le Ripault, BP 16
37260 Monts (France)
Tel. 33(0)2.47.34.41.85