AMBER Archive (2006)

Subject: Re: AMBER: NTT for production run

From: Vlad Cojocaru (
Date: Fri Mar 17 2006 - 03:16:36 CST

Dear David,

In fact, upon a bit of thinking I realized it doesn't make sense ...
When I did that test, I was too concentrated on the thermostat, and I
kind of forgot about the barostat ....

However, it was a useful discussion ...

Thanks both to you and Ross,

P.S. Maybe it would be useful to disallow ntt=0 with ntp=1, however, I
also think that if in such a test one gets the behavior I got it is also
very useful to realize ....

David A. Case wrote:

>On Thu, Mar 16, 2006, Vlad Cojocaru wrote:
>>I traced back that trajectory (it was ran sometime ago) and I have to
>>say "mea culpa" because in fact it was not ntt=0 but rather ntt=3 with
>>gamma_ln=0.0 (however, I believe it should be equivalent to ntt=0 ...
>>please correct me if I am wrong!).
>They are the same, but I did not realize you were trying to do a constant
>pressure simulation. With ntt=0, that would correspond to an "NPE" ensemble,
>which doesnt' make good sense. If you are doing constant pressure, you
>would not expect the total energy (and hence the temp.) to be conserved.
>(We should probably think about making the combination ntp=1 and ntt=0 not
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Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298

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