Re: Time of MD

From: edu (
Date: Thu Jun 29 2006 - 10:02:26 CDT

I have a protein in a water box (9250 total atoms). The PCs are connected in a window network and the time is :

using 1 PC: WallClock: 497.609009 CPUTime: 497.608002 Memory: 0 kB
using 2 PC: WallClock: 562.856018 CPUTime: 562.854980 Memory: 0 kB

  ----- Original Message -----
  From: JC Gumbart
  To: edu
  Cc: NAMD-L List
  Sent: Monday, June 26, 2006 11:33 PM
  Subject: Re: namd-l: Time of MD

  It is possible if the efficiency is really low.

  How many atoms are in your system? How are the two PCs connected? And what is the difference in times?

  On Jun 23, 2006, at 1:59 PM, edu wrote:


    When I run a MD simulation on 1 PC (using namd) the time involve in the process is lower than if I use 2 PC with Charmrun soft. żIt is possible?


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