AMBER Archive (2008)

Subject: Re: AMBER: nscm code

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Oct 10 2008 - 05:32:25 CDT

look in runmd.f, and if you search for nscm you should find the code
that uses it.

On Fri, Oct 10, 2008 at 1:05 AM, Naser Alijabbari <na3m_at_virginia.edu> wrote:
> Hello,
>
> I have been looking at the sander source code folder for Amber 8 and I am
> not recognizing any files that are about nscm or translation and rotation
> removal. Can someone point out the file/files. I am trying to understand
> what happens during translation and rotation removal during NVE ensemble
> (eventhough it should not be necessary to do this). From the archive I
> gather that for NVE (ntt not equal to 3) both translation and rotation are
> removed. Also any article or books that would be a help in understanding the
> code would be appreciated (I had a look at introductory books "Molecular
> modeling" by Andrew Leach and "Computational chemistry" by Christopher
> Cramer but did not recognize anything).
>
>
>
> In the ptraj code I see the rms function but my C is very rusty so can
> someone recommend source/sources for a better understanding.
> Thanks
> Naser
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