Re: NAMD job takes long time to finish 1 ns equilibration

From: Giacomo Fiorin (
Date: Tue May 05 2020 - 17:46:54 CDT

Hi, what did your PI, or the sysadmins of the servers recommend?

For pretty much everyone on this list, it would impossible to help without
- The size and type of your system.
- The architecture of the servers/cluster.
- What version and build of NAMD were you using and what commands you used
to select nodes and launch it.
You really need to provide a specific question about something you're stuck
with. There are some non-trivial details about running parallel codes (and
NAMD in particular) that it is fair to ask clarifications on, but you
should try first to do the basic troubleshooting steps yourself and report

Most importantly, although it is not unusual that some PIs send their
advisees straight to the mailing list for advice, it is somewhat perplexing
that despite touting his/her technical ability you still choose to ask
questions here.


On Tue, May 5, 2020 at 3:58 PM Khoualdi Asma Feriel <> wrote:

> Hello,
> I ran the equilibration for charmmGui generated input files for my
> membrane channel and ~1ns took me 8 days to finish on a two servers,
> knowing I am using max computational resources. Any suggestions as to why
> and how could I run it faster. My PI ran 200 ns of membrane protein in
> considerably less time.
> Thanks.

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2020 - 23:17:13 CST