VMD-L Mailing List

From: Bahaa Mostafa (bmostafa_at_sci.cu.edu.eg)
Date: Wed Dec 24 2014 - 23:42:56 CST

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> 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 system.
>
> Hope this helps.
>
>
> --
> Best,
> /A
> 

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