AMBER: question about a 20 kDa protein

From: David A. Case <>
Date: Sat, 18 Aug 2007 09:07:09 -0700

On Sat, Aug 18, 2007, Prem Prakash Pathak wrote:

First, please don't reply to (and copy!) a completely unrelated email: create
a new email if you wish to start a new topic.

> I am working solution structure of a 20kDa protein.
> I want to run a MD simulation.
> I have done a 100ps MD using sander, i.e. nstlim=50000 and dt=0.002,
> and ntpr=50 in explicite water system with charge neutralized.
> i wanted to know if these many steps are sufficient for a 20Kda
> protein to get it acceptable.

There is no way to know what you mean by the term "acceptable". You should
think about what you wish to learn from the simulation, and study papers that
address problems similar to the ones you are interested.

Having said that, 100ps is a very short amount of time, by modern standards.
Your protein is undoubtedly still relaxing away from the starting structure
towards the closest free energy basin in whatever force field you are using.


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Received on Sun Aug 19 2007 - 06:07:54 PDT
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