From: Mark Abraham (Mark.Abraham_at_anu.edu.au)
Date: Sat Feb 24 2007 - 10:20:05 CST
Pawel Weronski wrote:
> Dear NAMD experts,
> I would like to use the phosphate ions H2PO4(-1) and HPO4(-2) in my
> simulations. Is it possible to find the CHARMM force field parameters
> for them?
Only if someone has cared to develop parameters for them. The only
reliable way to do that is to follow the methodology that developed the
force field in the first place, which you find by reading the original
literature. If you don't want reliability, then do whatever you want.
> I found the parameters on the web site
> http://www.colby.edu/chemistry/webmo/mointro.html but I am not sure if
> they are fine for computations with NAMD.
Parameters in MD force fields are optimized to reproduce experimental
results in concert with the other elements of the force field. Results
from ab initio calculations for (say) bond lengths need not have any
correlation with the parameter for the minimum length for a zero bond
energy in an optimized MD force field. They do rate to be close, however.
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