Previous Thread
Next Thread
Print Thread
#149 10/09/03 11:35 AM
Joined: Sep 2003
Posts: 250
jb007 Offline OP
Forum Member
OP Offline
Forum Member
Joined: Sep 2003
Posts: 250
What's the rationale for choosing L-J parameters for metals? -
On comparison with Ne (rmin/2 = 1.53) in the CHARMM27 prm file with the nonbonded contact distance in the periodic system things look ok. However, for other metals, e.g. zinc, this trend is not obvious, rather it seems a bit ad hoc...so my question actually boils down to: To what extent should we use experimental values in defining force-field parameters?

jb007 #150 10/14/03 12:08 AM
Joined: Oct 2003
Posts: 783
A
Forum Member
Offline
Forum Member
A
Joined: Oct 2003
Posts: 783

Parameters for ions are typically based on reproduction of the experimental
free energy of solvation. In Charmm, the ion is assigned a formal charge
and then the LJ parameters are optimized to reproduce the free energy
of solvation. There is a Beglov and Roux paper in which they did this
for sodium. Finally, it should be noted that one set of LJ parameters for
an ion may not yield proper interactions with all types of functional
groups. A trick to get around this in charmm is the use of NBFIX for
to assign specific ion-atom LJ parameters that balance such
interactions.

alex


School of Pharmacy
University of Maryland
20 Penn Street
Baltimore, MD, 21201

Moderated by  alex, lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.5
(Release build 20201027)
Responsive Width:

PHP: 7.3.31-1~deb10u1 Page Time: 0.009s Queries: 18 (0.005s) Memory: 0.7288 MB (Peak: 0.7693 MB) Data Comp: Off Server Time: 2022-08-16 12:01:20 UTC
Valid HTML 5 and Valid CSS