Re: Protein collpasing problem!

From: Joshua Adelman (
Date: Mon Jun 29 2009 - 11:23:33 CDT

He Yandong,

As I suggested, search the namd-l archive and you will find several
threads discussing this topic. Additionally if you look in the
literature, you'll find that many papers on MD contain pertinent
information in the methods sections. As Axel warned, however, there is
no single way to do this and they are all system dependent. By trial
and error, you'll have to find what is correct for your system.

I am curious though how you are defining your 'equilibrium state' that
you say you obtain using both heating protocols (especially given that
your system is falling apart after a hand full of nanoseconds). This
in itself is a very tricky issue, and especially for large systems, it
is quite difficult to say definitively that your system is at
equilibrium. A first step is to say that your system appears stable
around a particular local minimum that you've placed it at, which
according to you, it does not. If your system was hoping between two
metastable states, or had transitioned to another state that, through
your intuition, seemed reasonable then this might be ok too, but in
your case your system is falling apart.


On Jun 28, 2009, at 11:12 PM, ydhuang2727 wrote:

> Hi,
> Yes, you are right, i should not have directly heated the protein up
> to 310K, which may cause problems. And i should heat gradually, to
> make the whole system approximately equilibrium. But from the namd
> tutorial, i did not find the more standard procedure, as you
> suggested, involving slowly heating system to the desired
> temperature. And i also feel surprise that you are so surprise,
> because i did not found anything wrong using "minimizing and then
> jumping to 310K", which is also definitely referred to in the namd
> tutorial.
> I myself previously used a loop in the .conf file to heat the
> protein, which refers to increase the heat source temperature up to
> desired temperature 20K by 20K that does look proper way but takes
> time, you know. Since heating directly up to 310K got the same
> equilibrium state as step by step, i chose the former to save cost.
> As your suggested standard procedure, i do have never seen anything
> about it.
> Will you please offer us some information available.
> Have you have any good advice on this problem.
> Good day!
> Yandong,
> 200万种商品,最低价格,疯狂诱惑你

Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley
Berkeley, CA 94720 USA

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