Re: increase the temperature step by step after minimization

From: Chris Harrison (charris5_at_gmail.com)
Date: Mon Aug 10 2009 - 05:01:08 CDT

What output do you get at the very beginning of and immediately before the
pairlist warnings, as well as immediately after?

Does it eventually die/crash or continue simulating once @ temp=310?

Chris

--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 217-244-1733
http://www.ks.uiuc.edu/~char               Fax: 217-244-6078
On Mon, Aug 10, 2009 at 12:27 AM, gurunath katagi <gurukatagi_at_gmail.com>wrote:
> Dear all,
> i am doing minimization and equilibration of o protein.. but after
> minimization, the temperature shoots up from 0 to 310 k. i think this will
> reduce the stability of the molecule. Instead iw ant to increase the
> temperutaure in steps of 310..
>
> the parameter s i included in my config file is:
> #temperaure increase
> reassignFreq            500
> reassignTemp            10
> reassignIncr            10
> reassignHold            310
>
> However i get the following error in the log file:
>
> Info: Pairlistdist is too small for 16 computes during timestep 103.
> Info: 16 pairlist warnings in past 1 steps.
> Info: Pairlistdist is too small for 2988 computes during timestep 104.
> Info: 2988 pairlist warnings in past 1 steps.
> Info: Pairlistdist is too small for 14 computes during timestep 107.
> Info: 14 pairlist warnings in past 1 steps.
> Info: Pairlistdist is too small for 227 computes during timestep 108.
> Info: 227 pairlist warnings in past 1 steps.
> Info: Pairlistdist is too small for 1652 computes during timestep 109.
> Info: 1652 pairlist warnings in past 1 steps.
> Info: Pairlistdist is too small for 152 computes during timestep 113.
> Info: 152 pairlist warnings in past 1 steps.
> Info: Pairlistdist is too small for 1408 computes during timestep 114.
> Info: 1408 pairlist warnings in past 1 steps.
> Info: Pairlistdist is too small for 782 computes during timestep 119.
> Info: 782 pairlist warnings in past 1 steps.
> Info: Pairlistdist is too small for 14 computes during timestep 122.
> Info: 14 pairlist warnings in past 1 steps.
> Info: Pairlistdist is too small for 235 computes during timestep 123.
> Info: 235 pairlist warnings in past 1 steps.
> Info: Pairlistdist is too small for 1337 computes during timestep 124.
> Info: 1337 pairlist warnings in past 1 steps.
> Info: Pairlistdist is too small for 47 computes during timestep 128.
> Info: 47 pairlist warnings in past 1 steps.
> Info: Pairlistdist is too small for 521 computes during timestep 129.
> Info: 521 pairlist warnings in past 1 steps.
> Info: Pairlistdist is too small for 417 computes during timestep 134.
> Info: 417 pairlist warnings in past 1 steps.
> Info: Pairlistdist is too small for 70 computes during timestep 138.
> Info: 70 pairlist warnings in past 1 steps.
> Info: Pairlistdist is too small for 290 computes during timestep 139.
> Info: 290 pairlist warnings in past 1 steps.
> Info: Pairlistdist is too small for 542 computes during timestep 144.
> Info: 542 pairlist warnings in past 1 steps
>
> Can any body help me to solve this problem?. thanks in adance
>
> --
> Gurunath M Katagi
> M.Sc (engg) Research student
> Supercomputer Education and Research Centre
> Indian Institute Of Science
> Bangalore
>

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