FEP, IONS, DUMMY atoms, LARGE numbers

From: Raul Araya Secchi (arayasecchi_at_hotmail.com)
Date: Mon Apr 17 2006 - 12:32:55 CDT

Dear NAMD users and Particulary Dr. Chipot :
Im performing some FEP calculations that involve a HIS to ASP transformation. I made an  hibryd of both aminoacids and have been testing in vacuo with interesting and precise results, but now I put the hybrid in a water box with an ion to balance the charges (going from neutral histidine to charged ASP) but some huge numbers appear and the simulation does not seem to equilibrate properly. So:
- I have only one Na+ ion present which should dissapear or become a dummy isnt it?
- should I fix both the Na+ and the Dummy in the same coordinates?
- Why even if a do so still large numbers appear?
- should I use an harmonic potential to restraint some positions between tha atoms of the hybrid?
- please any help will be most usefull...
Raul Araya
CGB - Universidad Catolica de Chile

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