Dumy atoms in FEP

From: Raul Araya Secchi (arayasecchi_at_hotmail.com)
Date: Mon Mar 13 2006 - 09:13:22 CST

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Hi NAMD users...

Im perfoming some FEP calculations in water and I need to make a charge
(ion) dissapear, but only its charge in order to keep the system neutral
(because the FEP goes from a charged residue to a neutral one). Should I put
a dummy atom in the same coordinates ans the dissapearing ion?
should I set tne dumy atom mass equivalent to that of the Ion or just keepit
without mass?
PLease help..

Raul Araya
CGB. Universidad Catolica de Chile
Chie

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