Re: NAMD2.7/MEtadynamics simulation analysis disparity

From: Giacomo Fiorin (
Date: Fri Apr 30 2010 - 09:16:17 CDT

Hello Neville, I assume you re-computed the distance between the two centers
of mass in VMD using the same selections (check also Felipe's suggestion,
probably it's not the case, but always worth making sure).

The other differences between the MD run in NAMD and the saved trajectory in
VMD are the PBCs: coordinates are not wrapped internally in NAMD, but they
may be wrapped in the output files, depending on what you specified in the
NAMD config file. Generally it's better to keep coordinates unwrapped at
all times, because the colvars module can't handle well a situation where
your protein is composed of multiple chains, not covalently bound together:
in that case, one subunit may appear at the other side of the unit cell. Is
your protein a single chain or multiple chains?

I didn't understand the last point, sorry: you wrote that there is a
difference of up to 1 Å between the variable computed in the two cases (NAMD
and VMD), which we need to find out why. Then you wrote that the variable
in NAMD suggests a displacement of about 6 Å, which is not consistent with
what you see in the trajectory: how can this be if the discrepancy was
always lower than 1 Å?


---- ----
Giacomo Fiorin
  ICMS - Institute for Computational Molecular Science
    Temple University
    1900 N 12 th Street, Philadelphia, PA 19122
---- ----

On Thu, Apr 29, 2010 at 9:49 PM, <>wrote:

> Maybe this is silly, but remember that in NAMD tha numbering scheme starts
> with 1 (as in the PDB) while in VMD starts at 0. This sometimes confuses
> some people when comparing data from the two sources.
> best
> felipe
> ----Mensaje original----
> De:
> Fecha: 29-04-2010 14:30
> Para: <>
> Asunto: namd-l: NAMD2.7/MEtadynamics simulation analysis disparity
> Hello guys,
> I have a question about running metadynamics with NAMD 2.7b2. I am running
> simulations between a ligand and a protein using metadynamics and NAMD2.7--e0cb4e887dd5bf8310048574e46f--

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:54:04 CST