AMBER Archive (2004)

Subject: AMBER: MD & folding

From: bybaker_at_itsa.ucsf.edu
Date: Tue Nov 02 2004 - 18:05:00 CST

('binary' encoding is not supported, stored as-is) Thanks, Carlos:

I will stop at here. As a beginner of MD, I am not confident on this
method. Amber is the only program I can utilize now. Since no one point
out any thing unusual in my inputs, I assume that I did standard runs. As
you suggested, I should look for answears from the articles.

Regards

Bo

On Tue, 02 Nov 2004 18:03:41 -0500 Carlos Simmerling wrote:

> Bo,
> using MD to study large conformational changes is a pretty
> advanced topic. modeling the effects of pH on stability is also
> very challenging. I think that it would give you a much better chance
> of success if you spend some time going through the articles written
> on these in the past few years to get an idea of what the issues
> are, and then send messages to the list that address specific
> problems or questions about the AMBER program. I just don't think
> that this email reflector is the best place to try to learn about this.
> For example, I think that comparing two ns-length MD simulations to
> answer questions about thermodynamic stability isn't the best
> choice, regardless of the force field and/or program that you use.
> there are many articles where people have gone into these ideas
> in depth, after lots of careful writing and good references. That
> will be much more useful to you than the kind of short answer that
> people are likely to be willing to write in an email.
>
> Don't take this as a criticism, just a suggestion about how to get the
> information that you want.
> Carlos
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu