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

Marc Baaden baaden at smplinux.de
Wed May 18 12:28:49 CEST 2005

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 ?

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 ?

phuong at theochem.uni-frankfurt.de said:
>> this problem was discussed by Karplus et al. in the paper J. Comp. Chem. 16,
>> 1522-1542 (1995) 

I might not have read through that thoroughly enough; are you refering
to the part "Reduced basis normal modes procedure" ? It seemed to me
that this applies if you want to look at specific motions (eg torsions
only) but not in order to reduce from all-atom to eg Ca only. Maybe I got
that wrong.

Thanks again,

 BioMolSim meeting 2&3 Sep 2005: http://www.iecb.u-bordeaux.fr/satellite2005/

 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden at smplinux.de      -      http://www.baaden.ibpc.fr
 FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217

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