Re: Protein collpasing problem!

From: Joshua Adelman (
Date: Fri Jul 03 2009 - 10:55:53 CDT

Hi Yandong,

Again, please email the list rather than me directly.

Judging stability can be difficult, and there is no one way or
'correct' way to do so. The most common measure is to look at the the
RMSD of your protein as a function of time to see if that value has
leveled off (there is a nice tool in VMD that can do this). Others
look at secondary structure content, while others take a particular
quantity that is of interest in their project (e.g. the center-of-mass
distance between two domains), and check if there is drift over the
coarse of the trajectory. None of these are perfect, but this should
get you started. You're simulating a fairly large system, so this is
going to be tricky regardless of how you do this, and sampling is not
on your side.

Also, be sure to search the literature and see what other have done
previously. Of course, you should also check the .log file to be sure
that your system is behaving as you expect in terms of the ensemble
that you've chosen to run your simulation in.

Best wishes,

On Jul 3, 2009, at 12:39 AM, ydhuang2727 wrote:

> Hi, Josh,
> Forgive my reply so late.
> Some points of your comment help me much.
> Now that i can't simply assert one protein is stable just from VMD
> that displaying MD trajectory. I naturally have a question that how
> do i judge whether my system is stable or not from output file .log
> or some other paths.
> Thanks again!
> Good day,
> Yandong,
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