Re: Working on cluster to do umbrella sampling

From: Michael Grabe (
Date: Mon Nov 22 2004 - 13:47:14 CST

Hello Enrico,

I have done umbrella sampling with NAMD.

You need to use the TCL interface to define
the umbrella potentials and then just do normal
MD after that. As far as I know NAMD does not have
any kind of routine for unbiasing the potential so
I read my DCDs into MATLAB where I have my own
WHAM code written. It is all pretty easy to do once
you have things set up.

If you want a simple tcl script, i can send one to you
at some point in the near future. Let me know.


On Friday, November 19, 2004, at 02:39 AM, Enrico Piccinini wrote:

> Hi. I have some questions for experts...
> 1) I'm trying to install NAMD on a beowulf cluster, can someone tell me
> which of the pre-compiled version works better?
> 2) I'm not sure if this is the right one, but Linux-i686-Scyld-TCP
> works. When I allocate 4 processors on the cluster with mpirun -np 4
> namd2 conffile > logfile the output i get is the following and only 1
> processor seems to be used.
> Info: NAMD 2.5 for Linux-i686-Scyld-TCP
> Info:
> Info: Please visit
> Info: and send feedback or bug reports to
> Info:
> Info: Please cite Kale et al., J. Comp. Phys. 151:283-312 (1999)
> Info: in all publications reporting results obtained with NAMD.
> Info:
> Info: Based on Charm++/Converse 050612 for net-linux-scyld-tcp-icc
> Info: Built Fri Sep 26 17:33:55 CDT 2003 by jim on
> Info: Sending usage information to NAMD developers via UDP. Sent data
> is:
> Info: 1 NAMD 2.5 Linux-i686-Scyld-TCP 1
> affinito
> Info: Running on 1 processors.
> Is this normal and i am missing something?
> 3) The last one is my big problem: has anyone ever done umbrella
> sampling with namd?
> Thank you
> Enrico
Michael Grabe, Ph.D.
Genetics Development & Behavioral Science Building
1550 4th Street, GD 481
San Francisco, CA 94143-0725
tel: ++ 415.476.0421

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