From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Sat Feb 24 2007 - 15:42:55 CST
Define "reliability", that is such an objective term. What is reliable to one, is unreliable to another.
Let's say I developed a force field, and let's say it reproduced any physical observable you could think of for a wide range of molecules. I would say it was reliable, yet you and the rest of the scientific community might disagree.
Richard L. Wood, Ph. D.
Cockeysville, MD 21030
----- Original Message ----
From: Mark Abraham <Mark.Abraham_at_anu.edu.au>
To: NAMD Users List <namd-l_at_ks.uiuc.edu>
Sent: Saturday, February 24, 2007 11:20:05 AM
Subject: Re: namd-l: force field for H2PO4- and HPO4(-2) ions
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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