[gmx-users] Normal Mode Analysis on Calphas only ??
baaden at smplinux.de
Wed May 18 12:28:49 CEST 2005
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
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
More information about the gromacs.org_gmx-users