Re: Reassign Temp during the Production Run

From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Thu Jul 16 2009 - 13:04:03 CDT

According to your input, you are reassigning a temp 310 every 500 steps,
creating a periodic redistributing of velocities. If anything, I'd except
this to destabilize rather than stabilize, as this will prevent some areas
of your system from equilibrating into an "ordered" state. Unless your
expected salt-bridge cleavage results from a cumulative process (that was
disturbed by reassigning velocities), then I doubt this is the cause.

But that's just my 2 cents.

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 12:32 PM, twshen <tshen_at_uh.edu> wrote:
> 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 <http://www.ks.uiuc.edu/%7Echar>
>     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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