Re: Lennard-Jones Potential

From: Victor Kwan (vkwan8_at_uwo.ca)
Date: Sat Feb 23 2019 - 12:41:34 CST

There are many ways to deal with divalent cations. AFAIK 12-6-4 is supported by AMBER, not sure if it is supported in NAMD. For NAMD, your best bet is probably CUFIX.


Victor

On Sat, Feb 23, 2019 at 1:11 PM McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>> wrote:

Excellent, this helps a ton. What do you think of the C4 parameter in the 12-6-4 LJ picture I included, is there a way to specify that too? That is important for the metal ions energy calculation.


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 11:09:00 AM
To: McGuire, Kelly
Cc: namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>
Subject: Re: namd-l: Lennard-Jones Potential

Looks like it is

<ATOM TYPE 1> <ATOM TYPE 2> <EPSILON> <R_MIN> <1-4 EPSILON> <1-4 R_MIN>

per https://www.charmm.org/charmm/documentation/by-version/c40b1/params/doc/parmfile/

Victor

On Sat, Feb 23, 2019 at 1:02 PM McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>> wrote:

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<mailto:vkwan8_at_uwo.ca>>
Sent: Saturday, February 23, 2019 11:00:36 AM
To: McGuire, Kelly
Cc: namd-l_at_ks.uiuc.edu<mailto: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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