VMD-L Mailing List
From: Bahaa Mostafa (bmostafa_at_sci.cu.edu.eg)
Date: Sun Dec 28 2014 - 00:39:47 CST
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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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- Next message: sunyeping: "the usage of measure bond"
- Previous message: Kazem Sepehrinia: "density profile install"
- In reply to: Josh Vermaas: "Re: non-bonded interactions"
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