AMBER Archive (2007)

Subject: Re: AMBER: Can I set harmonic constraints in SMD simulations ?

From: David A. Case (case_at_scripps.edu)
Date: Sat Sep 15 2007 - 11:59:33 CDT

On Sat, Sep 15, 2007, James W wrote:

> This is my setting shown below . Could you tell me it reasonable ?

I think this is a pretty general question to expect to be answered on the
mailing list. Why not set nstlim to a short value, ntpr to 1, run it, and
examine the output closely? The sander output gives a lot of information
about what it is doing.

It is essential that you learn how to do this *yourself*, if you are ever to
have any success with molecular simulation.

For example, if you actually run your test case, you would see that no
constraints were being applied (because you did not set ntr to 1).

...dac

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