Re: Reassign Temp during the Production Run

From: twshen (tshen_at_uh.edu)
Date: Thu Jul 16 2009 - 12:32:40 CDT

Hi,

  I'd like to measure the stability of salt bridges on the surface
of my protein (in water). What I expect to see is that the salt
bridge should break and reform frequently. However, I saw the
salt bridge is quite stable. Is "reassignTemp" the problem?
Thank you.

Tsaiwei Shen

On Thu, Jul 16, 2009 at 12:17 PM, Chris Harrison<char_at_ks.uiuc.edu> wrote:
> Um.....yeah.
> What property do you want to measure from the multi-temp simulation?
>
> 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 Thu, Jul 16, 2009 at 12:04 PM, twshen <tshen_at_uh.edu> wrote:
>>
>> Dear all,
>>
>>  I found that I reassign the temperature, in other words,
>> velocities, every 500 steps during the production run.
>> Since "reassignTemp" should be turned off during the
>> production run, I am wondering if this can make a
>> difference in the trajectory. Thank you very much.
>>
>> Here are my simulation parameters for the production run

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