Re: Re: NAMD: Exiting Prematurely

From: Arun Krishnan (krishnan_at_ttck.keio.ac.jp)
Date: Wed Aug 15 2007 - 20:19:17 CDT

Dear Jeff,

Thanks. That's what I did.. changed it to 1fs and it seems to be running
now.. nearing the 0.5 ns mark. I guess
that's the key when running at high temperatures.. at least for NAMD. I
recall reading a post by an ex-member of the Daggett group who suggested
that he'd be very surprised if we could run upto 1ns using 2fs time step at
higher temperatures in NAMD..
Something to do with the integration scheme it seems.

Cheers,

Arun

On 8/15/07, Jeffrey J. Potoff <jpotoff_at_chem1.eng.wayne.edu> wrote:
>
>
> Dear Arun,
> Try using a smaller timestep, such as 1.0 fs (or even 0.5 fs)
> until the system is equilibrated.
>
> Regards,
> Jeff
>
> ======================================================================
> Jeffrey J. Potoff jpotoff_at_chem1.eng.wayne.edu
> Associate Professor Wayne State University
> Department of Chemical Engineering and Materials Science
> 5050 Anthony Wayne Dr Phone:(313)577-9357
> Detroit, MI 48202 Fax: (313)578-5815
> http://potoff1.eng.wayne.edu
> ======================================================================
>

-- 
***********************************************
Arun Krishnan, Ph.D,
Assistant Professor,
Institute for Advanced Biosciences,
Keio University,
Center Building,
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Japan
Phone: +81 (0)235-29-0824
Email: krishnan_at_ttck.keio.ac.jp
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