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

[Wei Fu]

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?

Thanks!!!
           
Fu, Wei

2004-01-28
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  Wei Fu (Linda)
  Postdoctoral Research Associate
  Department of Biology and Biochemistry 
  University of Houston
  4800 Calhoun Rd. HSC #402C
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  Phone:713-743-8355(o)  713-795-9270(h) 
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  Email: fuwei at adrik.bchs.uh.edu
  http://adrik.bchs.uh.edu/~fuwei/
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