AMBER Archive (2006)

Subject: Re: AMBER: WHAT IF CHeck after MD

From: David Mobley (dmobley_at_gmail.com)
Date: Thu Sep 28 2006 - 17:58:32 CDT

Energy landscapes are typically fairly rough with large energetic
barriers. If your phi-psi angles are "bad" but separated by huge
barriers from the "good" angles, just running MD for a while probably
won't solve the problem, as the relevant atoms will be kinetically
trapped on the wrong side of the barrier. You might try replica
exchange, or some sort of Monte Carlo technique.

David

On 9/28/06, Fenghui Fan <fenghui_fan_at_yahoo.com> wrote:
> Dear all,
>
> I hope I can use MD to opitmize a structure because
> the original structure is a computational modelling
> structure and contains a lot of poor quality part for
> example poor phi-psi angles. However I find the
> COORdinates of the MDed structure at different MD
> times does not improve significantly. What is more,
> some check standards chnage worse.
>
> Will you please give me an explaination on these?
>
> I am looking forward to getting your message.
>
> Best regards.
>
> Fenghui Fan
>
>
>
> __________________________________________________
> Do You Yahoo!?
> Tired of spam? Yahoo! Mail has the best spam protection around
> http://mail.yahoo.com
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu