Using NAMD for Metropolis Monte Carlo conformational searches

From: Ajasja Ljubetič (
Date: Tue Nov 09 2010 - 09:12:29 CST

Dear NAMD users,

would it be possible to use NAMD in Metropolis Monte
 (By MMC I mean, that the probability of transition to the next
configuration is weighted by the energy difference between the

The simplest solution would be to generate a new conformation and run namd
for this one file and then parse the log file. But I think this would
introduce significant overhead (since NAMD would have to parse the psf and
pdb for each frame etc.)

Currently I'm using

coorfile open dcd $dcdin
while { ![coorfile read] } {
  run 0
coorfile close

to do random conformational searches. This works nicely, since I can
pre-generate all conformations.

I'm thinking of using a socket for communicating with NAMD. Then I could
signal NAMD that a new conformation is available using a socket and do
 coorfile open dcd frame_xxx.dcd
coorfile read
run 0
coorfile close

Or, better yet, if the file is not locket by coorfile open, I could even
append to the same file (thereby avoiding coorfile open and coorfile close for
every frame).

I have to main questions:
1) Is it possible to send the total energy calculated by run 0 to the socket
channel instead of only outputing it to the log (and forcing me to parse
this output for every frame).
2) Is there a better way to do this kind of conformational searches?:)

Thank you,
Ajasja Ljubetič,
young researcher,
Condensed matter department,
Institute Jozef Stefan,
Ljubljana, Slovenia

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:54:44 CST