Re: Utilizing Amber6 on Linux Cluster

From: Margaret Cheung <>
Date: Wed 22 Aug 2001 10:23:40 -0700 (PDT)


I'm sorry to intrude your conversations. But the following message caught
my eye. I was wondering if anyone has posted benchmarks for running
parallel MD in both NAMD and sander. Thank you very much.

Sincerely yours,

> >I then successfully compiled amber6.
> >When running sander if I set ntc=3, the job bombs and I get the message
> >for this parallel version only works for ntc < 3
> >Is this legitimate?
> Apparently so. Have you looked at NAMD? It can read AMBER prmtop and prmcrd
> files but is a much better MD implementation, written in C/C++, is much faster
> on Linux clusters w/ 100BaseT, and is freely available.
> Dave
Received on Wed Aug 22 2001 - 10:23:40 PDT
Custom Search