Re: Structure size limitation in NAMD

From: Chris Harrison (
Date: Wed Jan 29 2014 - 23:41:09 CST

Well, hoss,

I don't read the email listserv as frequently as I used to, but the
HIVcapsid isn't even close to the max # atoms NAMD will support now.
 Systems in excess of 150 million atoms have been done. See the BlueWaters
benchmarks. As mentioned, RAM constraints during setup of extremely large
systems (ie >10 million) are a principal problem for the common user.

MORE IMPORTANTLY: The trick isn't getting a numerical
"oh-my-system-is-huge" number of atoms. Instead it's about getting a
system that is that large, and yet "stable enough" to perform the
calculations/measurements you want to do on the timescale in which you
interested. Best of luck; may the odds be in your favour.


On Wed, Jan 29, 2014 at 10:00 PM, Axel Kohlmeyer <> wrote:

> On Wed, Jan 29, 2014 at 9:36 PM, Nithyanan Annamalai
> <> wrote:
> > Hi, I'm still at learning in using NAMD for my research. My research is
> > focus on molecular dynamic simulation of a dimer protein. I want to know
> is
> > it possible for me to run a dimer structure in NAMD?
> > And if there is a limitation for size of protein structure, may i know
> how
> > much the applicable size of structure that can be run using NAMD.
> you probably won't have a computer large enough to run the largest
> possible system. check out this link (which is featured on the NAMD
> homepage).
> >
> > I'm sorry if the question i posted here sounds to noob. Hopefully there
> are
> > good hearts willing to help me.. Thank you very much for your kindness.
> --
> Dr. Axel Kohlmeyer
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.

Chris Harrison, Ph.D.

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