MD with 3-site CO model

From: Nadia Elghobashi-Meinhardt (nelgho_at_gmail.com)
Date: Wed Mar 04 2020 - 08:24:51 CST

• Next message: soodabeh ghaffari: "Re: adding peptide constraint in NAMD configuration file"
• Previous message: Giacomo Fiorin: "Re: adding peptide constraint in NAMD configuration file"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi everyone,
I am using a 3-site CO model (of Straub&Karplus, with a dummy atom of zero
mass) with the charmm36ff to simulate the diffusion of a rigid CO molecule.
I am not sure of what combination of force constants / constraints/ heating
protocols to use.
With my current setup, NAMD complains of high velocities for the dummy atom.
Does anybody have any tips?
Thank you!

Nadia
Technical University Berlin

• Next message: soodabeh ghaffari: "Re: adding peptide constraint in NAMD configuration file"
• Previous message: Giacomo Fiorin: "Re: adding peptide constraint in NAMD configuration file"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2020 - 23:17:12 CST