From: Bahaa Mostafa (bmostafa_at_sci.cu.edu.eg)
Date: Sun Dec 28 2014 - 00:39:47 CST

thank you Josh, thank you Ashar, that exactly what i miss,
just to be absolutely clear about this point, for the hypothetical
a-b-c-d-e fragment , if (a) has two LJ i should use the first one for the
(a,e) pair and the second one for the (a,d) pair, but if (a) has only one
LJ , i will use it for both (a,d) and (a,e) pairs, is that true,

regarding combination rules:
Rminij = Rmin/2i + Rmin/2j
epsij = sqrt(epsi * epsj)

occasionally, could i use the same switching function for both vdW and
electrostatic interactions?

On Fri, Dec 26, 2014 at 5:52 AM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> 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.
> -Josh Vermaas
>
> 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> 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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*Disclaimer:* This E-mail represents the views of its author only and does 
not necessarily reflect the opinions of Faculty of Science (*SCI 
<http://www.science.cu.edu.eg>*). We do not assume responsibility for any 
loss, damage (including direct, indirect, punitive, special, or 
consequential loss or damage), which you may directly or indirectly suffer 
from this email or its contents or through the ways of handling this email 
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does not necessarily mean that *SCI* <http://www.science.cu.edu.eg>owns 
these materials either partially or fully. In addition, any service that is 
provided by and/or through *ITU(SCI) <http://itu.sci.cu.edu.eg>*, without 
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them either by negligence, misconduct, misuse and/or abuse. And even though 
our network checks and scans all e-mails to make sure it is safe and does 
not contain any viruses,Trojans or Spywares , it is also the responsibility 
of the recipient to ensure that the e-mails and attachments therein are 
free of any danger, and *SCI <http://www.science.cu.edu.eg>*will take no 
responsibility for any damages or losses that may arise as a result from 
the misuse or the presence of viruses or spyware sent through messages or 
web services.