[gmx-users] Effect of atomic charge on bonding parameters

[Justin Lemkul]

On 4/2/20 2:45 PM, Neena Susan Eappen wrote:
> Hi Justin,
>
> What is the criteria for opls bond types?

I don't understand the question. Nonbonded and bonded atom types can be 
separate (this is uncommon, but something that OPLS does) because bonded 
interactions may be more transferable than nonbonded paramters. I have 
no idea why OPLS has opls_237 and opls_238 when they have the same 
bonded type and same LJ parameters. They're effectively identical so 
this is probably a very poor example when trying to learn how the force 
field works.

If you're trying to generate a topology for some new species, try the 
LigParGen server rather than going about it manually.

-Justin

> Thank you,
> Neena
> ________________________________
> From: Neena Susan Eappen
> Sent: Wednesday, April 1, 2020 12:05 AM
> To: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] Effect of atomic charge on bonding parameters
>
> Hello gromacs users,
>
> Following two atoms (opls_ 237 and 238) have different atomic charges, but same bond type and thereby same parameters in the ffbonded.itp file. Is the effect of charge on bonding ignored? Is that possible?
>
> ; name       bond_type     mass        charge   ptype          sigma      epsilon
> opls_237     N    7        14.00670     -0.760       A      3.25000e-01  7.11280e-01
> opls_238     N    7        14.00670     -0.500       A      3.25000e-01  7.11280e-01
>
> (Taken from ffnonbonded.itp file)
>
> Thank you,
> Neena

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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