Re: Lennard-Jones Potential

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Sat Feb 23 2019 - 12:02:18 CST

Ah I see, thank you Victor. Do you have any example code for NBFIX and a second well depth and minimum radius specification? I searched, but couldn't find any...

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: Victor Kwan <vkwan8_at_uwo.ca>
Sent: Saturday, February 23, 2019 11:00:36 AM
To: McGuire, Kelly
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: Lennard-Jones Potential

Hi Kelly,

>From the charmm forcefield manual:

The NBFIX section (H) allows VDW interactions between specific atom pairs to be modified. This is done by specifing the 2 atom types followed by the well depth and the minimum radius (not (minimum radius)/2 as in NBOND). A second well depth and minimum radius may be specified to determine the 1-4 interactions.

Victor

On Sat, Feb 23, 2019 at 12:38 PM McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>> wrote:

Hey Victor, thanks for the response. Is NBFIX a command or in a file?

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: Victor Kwan <vkwan8_at_uwo.ca<mailto:vkwan8_at_uwo.ca>>
Sent: Saturday, February 23, 2019 10:35:49 AM
To: namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>; McGuire, Kelly
Subject: Re: namd-l: Lennard-Jones Potential

See NBFIX

Victor

On Sat, Feb 23, 2019 at 12:34 PM McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>> wrote:

I found some literature where the Lennard-Jones potential was modified (another term was added) to model certain atom types better. Is there a way to modify or add a term to the Lennard-Jones potential in NAMD?

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

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