[gmx-users] Normal Mode Analysis on Calphas only ??

[Berk Hess]

>From: Marc Baaden <baaden at smplinux.de>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] Normal Mode Analysis on Calphas only ?? Date: Wed, 
>18 May 2005 12:28:49 +0200
>
>
>Hi again,
>
>thanks for all those helpful comments, I see a lot clearer now.
>So it looks like we'll most probably code up Berk's formula.
>Berk, is there a reference for it ?

I don't think so, but I'll ask around to be sure.

>
>On the practical side it would seem to me that one could just
>add an option -n for an index file to g_nmeig and if present
>consider the given index as the interesting particles applying
>the transformation by Berendsen. Is this the way to go ?

Yes.

Note that the CVS version contains much more efficient
linear algebra routines. So you might want to do this
in the CVS code.

Berk.

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