dummy atoms and FEP

From: Raul Araya Secchi (arayasecchi_at_hotmail.com)
Date: Thu Apr 06 2006 - 11:36:57 CDT

Dear NAMD users
Im still fighting with the FEP....but new quiestions arise all the time....
I need to make a Na ion dissapear from my system to keep it neutral (for PME) but I dont know if I should put just a DUM atom (using the charmm 22 parameters and topologies) with 0 charge 0 mass or a Na ion without charge (dont know well how to do this). The reason for my question is that I only need the charge to dissapear in my FEP, ant the DUM atom has tha radii of the H atom I think....
Is that simple, replace the Na for a DUM or it requires some other trick?
please Help
And again: Have any one used or is familiar with the Overlap Sampling method for FEP? or the Bennet method?
Raul Araya
CGB-Universidad Catolica de Chile

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