[gmx-users] Re: multi cpu problem (Anton Feenstra)

Wei Fu fuwei at adrik.bchs.uh.edu
Wed Jan 28 21:48:00 CET 2004

Hi, Anton,

    As you stated in the "Subject: Re: [gmx-users] errors depending on (lack of) solvent",  the limitation is in solving (distance) constraints (e.g., for constant bondlengths). That means that I can run SD with muilt processors when setting the "constraints = none"?

I have done some SD tests on my protein by "constraints = none", the results are:
it runs when submitting job directly (interactive) with 2 cpu
but it can not run when submitting job to background (by nohup) with 2 cpu.

when set parameter to "constraints = hbonds"
it can't run SD simulation on my protein with 2 cpu on both interactive and background mode, but SD can run with 1 cpu.

   So, whether this means I only can run SD with 1 cpu?  My proteins consist of 423 residues, 3431 atoms. How long it will take to do a simulation of 500 ns with 1 cpu? 

   By the way, whether there is some way to run SD on multiple cpu?

Fu, Wei

  Wei Fu (Linda)
  Postdoctoral Research Associate
  Department of Biology and Biochemistry 
  University of Houston
  4800 Calhoun Rd. HSC #402C
  Houston, TX 77204-5001   USA
  Phone:713-743-8355(o)  713-795-9270(h) 
  Email: fuwei at adrik.bchs.uh.edu

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