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#1 2019-03-06 11:33:04

julieborah66
Member
Registered: 2018-09-17
Posts: 26

Total sum of charge of CM5

Hello Sir,

I am using an octamer (consist of 104 atoms) that has a first, middle and end residue. The CM5 charges are being generated by Multiwfn and total of the CM5 charges is zero,now I want to apply the charges to a long molecule (1162 atoms) and want to do a molecular dynamics simulation, then I use the charges for front residue for octamer to long molecule, middle residue for octamer to long molecule and so on, and now obviously the charges of the long molecule isn't a zero (for floating numbers), which is a pre-requisite for doing molecular dynamics simulation (the total charge of the molecule should be neutral), So, if i make small changes in the fourth decimal of the charge file in md, and get it a zero, am I proceeding in the right way? ( I did change the fourth decimal because playing up with parameters isn't allowed) .

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#2 2019-03-06 18:12:47

sobereva
Tian Lu (Multiwfn developer)
From: Beijing
Registered: 2017-09-11
Posts: 244
Website

Re: Total sum of charge of CM5

Hi,

I am unable to capture your meaning, and unable to imagine the basic character of the "octamer" and "long molecule".

For MD purpose, RESP is evidently preferred over the CM5 charge, because RESP charges have much better ability to reproduce ESP around vdW surface. Also, during fitting the RESP charges you are able to constraint the total charge of specific fragments, so that you can then easily transfer the atomic charges in the fragment to analogous system.

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#3 2019-03-08 06:48:16

julieborah66
Member
Registered: 2018-09-17
Posts: 26

Re: Total sum of charge of CM5

Sir, apologies for not making it understandable, by "octamer" I mean "two monomers "of the polymer used for calculation and by "long molecule" I mean  "25 monomers" of the polymer used. I know RESP fitting is better than CM5, but for comparison of charges I do have to consider all the charges.
I took an octamer for calculation, since it is the best representation of the polymer by some experimental results. Now, the problem that arises is getting a neutral condition, So, I made some small adjustments to the charges obtained by DFT in the fourth decimal of the charges of atoms to make it a neutral for MD purpose.
Is there any better way than this to obtain CM5 charges for the polymer (long chain)?

Last edited by julieborah66 (2019-03-08 08:02:02)

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#4 2019-03-08 19:12:58

sobereva
Tian Lu (Multiwfn developer)
From: Beijing
Registered: 2017-09-11
Posts: 244
Website

Re: Total sum of charge of CM5

If just adjusting the resulting CM5 charges at the fourth decimal will satisify your purpose, then this treatment is reasonable, because the artificial perturbation is so small. Probably what you want to realize is constrainting the sum of CM5 charges of specific fragment to zero, unfortunately, this purpose cannot be realized in the framework of CM5 method in principle.

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#5 2019-03-08 20:13:55

julieborah66
Member
Registered: 2018-09-17
Posts: 26

Re: Total sum of charge of CM5

Thank you Sir for helping me out. I my full of gratitude.

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