From: curcio (r.curcio_at_bioc.unizh.ch)
Date: Thu Mar 09 2006 - 11:48:41 CST
Hi all,
I have a question concerning the usage of locally enhanced sampling (LES ) as
provided by NAMD:
Is there any reason why not using LES together with the PME-method?
If no, i.e. it is fine to combine LES with PME, then how should "replicated"
charges (i.e. multiple copies of a charged part, e.g. of the sidechain of a
lysine) be taken into account when neutralizing the charge with counterions?
Imagine there are five copies of the sidechain of a lysine instead of only one
- how many negatively charged ions should be used to account for the charge
of this replicated lysine? Five negatively charged ions or is one already
sufficient for instance because the electrostatic interaction is also divided
by five?
Thanks for your help,
Raffaele
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