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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