Re: force field for H2PO4- and HPO4(-2) ions

From: Richard Wood (
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 Richard L. Wood, Ph. D. Computational Chemist Cockeysville, MD 21030 ----- Original Message ---- From: Mark Abraham <> To: NAMD Users List <> 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 > 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. Mark ____________________________________________________________________________________ We won't tell. Get more on shows you hate to love (and love to hate): Yahoo! TV's Guilty Pleasures list.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:24 CST