VMD-L Mailing List
From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Thu Dec 25 2014 - 21:52:34 CST
All 1-4 pair combinations contribute to the VDW terms, just like how all
the pairs contribute to electrostatics. The difference is that certain
atomtypes use different parameters for when they are interacting in a
1-4 pair than they do with a general non-bonded pair. These atomtypes
have two sets of nonbonded parameters, the first is the standard
long-distance pair, and the second is the parameter set used for 1-4
pairs. I hope you are familiar with the combination rules CHARMM uses...
Otherwise you are in trouble.
On 12/24/14 11:42 PM, Bahaa Mostafa wrote:
> thank you ashar for interest,
> but i don't use NAMD, i can't install it on my PC (windows) at all, i
> have VMD installed correctly, but i don't know if it calculates energy
> with charmm force field,
> so i have to do calculations myself, i think all terms are going well,
> till now but the nonbonding terms, i think some missing information
> about them cause my calculations not accurate, hope you can answer my
> question or recommend me a source to answer it,
> my question again :
> some atoms have 1-4 LJ parameters , but others don't have,
> what does it mean ?
> does it mean these atoms have no vdW interaction?,
> or does it mean i should use the not 1-4 LJ parameters instead of
> these missing parts ?
> best wishes,
> On Wed, Dec 24, 2014 at 2:43 PM, Ashar Malik <asharjm_at_gmail.com
> <mailto:asharjm_at_gmail.com>> wrote:
> how can i calculate 1-4 vdW interaction energies for those
> atoms don't have 1-4 LJ parameters,
> Three things:
> 1) You need to do some reading about what the force field terms
> are and what do they actually mean?
> 2) What 1 - 4 means?
> 3) When you run a simulation/minimization energy terms are printed
> out to the log file. vdW is a form of NONBONDED energy and has its
> own column. If you want to do the calculation not on the entire
> system but a small selection of atoms - look at ATOMSELECT to make
> the selection and use NAMDENERGY to calculate the energy of your
> Hope this helps.
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