virtual and heavy hydrogens in NAMD

From: rebeca_at_mmb.pcb.ub.es
Date: Wed Jul 23 2008 - 09:22:12 CDT

Hello,
Does anybody know if there is an option in NAMD analogous to “-vsite hydrogens”
and / or “-heavyh” (in Gromacs)?
The first one removes hydrogen and fast improper dihedral motions, removing
angular and out-of-plane motions. The mass of all atoms that are converted into
virtual sites, is added to the heavy atoms.
The second also slows down the dihedral motion, increasing the hydrogen-mass by
a factor of 4. The increase in mass of the hydrogens is subtracted from the
bonded (heavy) atom so that the total mass of the system remains the same.

Are similar options included in NAMD? I have looked into the manual and I have
not found anything.

Thank you very much for your help in advance.

Rebeca García Fandiño
Parc Cientific de Barcelona
rebeca_at_mmb.pcb.ub.es

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