From: Ramon Mendoza Uriarte (ramendoza_at_uchicago.edu)
Date: Thu Feb 25 2021 - 15:26:33 CST
Hello,
Sorry for the spam, however I do not think my previous email went through.
-Ramon
________________________________
From: Ramon Mendoza Uriarte
Sent: Wednesday, February 24, 2021 7:15 PM
To: NAMD list <namd-l_at_ks.uiuc.edu>
Subject: CHARMM Parameter question
Hello NAMD community,
I am playing with the NBFIX parameters for the interaction between a single potassium ion and the oxygen of the TIP3P water molecule. Currently, I am struggling to understand how the CHARMM parameters are used in a standard run, for instance, without the NBFIX parameters. For example, I am performing a minimization with the attached force field parameters. In this parameter file the following parameters for water and potassium ions are contained within:
OT 0.0 -0.1521 1.7682
POT 0.0 -0.0870 1.76375
and thus, from the minimization I get the following averages:
pair Total Distance (K+- O)
Energy (Å)
(kcal/mol)
K - water -20.2 2.62
>From my understanding the Lorentz-Berthelot combination rules are used in determining the LJ parameters. For instance, the parameters for the interaction between the oxygen and potassium ion would be as follows:
Emin = sqrt(0.1521 * 0.0870) = 0.115033
Rmin = 0.5 * (1.7682 + 1.76375) = 1.7659
Now, if I were to specify this as an NBFIX parameter I get the following:
pair Total Distance (K+- O)
Energy (Å)
(kcal/mol)
K - water -75.8 1.18
However, I do not understand why the two give different outputs for the Total Energy and the distance between the potassium and oxygen atoms. So, basically my question is how are the LJ parameters being combined in NAMD? I have attached my config file and the unmodified and modified parameter files as well. Any assistance would be appreciated!
Thank you,
Ramon
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