Re: AMBER: MD & folding

From: Carlos Simmerling <>
Date: Tue, 02 Nov 2004 18:03:41 -0500

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 L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web:
Stony Brook, NY 11794-5115 E-mail:
=================================================================== wrote:

>Hello, Bimo:
>Thank you very much for your advices.
>It worthy to try running the MD at a longer time, such as 10 ns. This
>might take about two months to finish. I am not sure I can do this. I
>will give a try.
>On the other hand, some literatures, such as Alonso et al 2001, showed
>significant conformation changes on ptotein conformation during a 10 ns
>MD run at pH 2.0. And the change was observed even at the first 2 ns
>runs. In my cases, the two runs at different pHs are almost identical. I
>am wondered if Amber force fields are suitable for such kind of unfolding
>By mistake I sent my input files as a Word attachment. Soory about that.
>I have included the files at the end of this message.
>All the bests.
>Here is the input files:
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Received on Tue Nov 02 2004 - 23:53:00 PST
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