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Re: [lammps-users] lj parameters
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# Re: [lammps-users] lj parameters

 From: Stefan Paquay Date: Wed, 13 Sep 2017 11:26:11 -0400

Most of the confusion seems to arise over whether or not there was a typo in the article. Maybe it makes more sense to contact the authors to double-check with them. I can't imagine this not being a typo, but hey, you never know.

If it is a typo and they meant to write epsilon*((r_min/r)^12 - 2(r_min/r)^6), then yes, you need to perform the conversion from r_min = 2^(1/6) sigma to sigma, because LAMMPS uses the 4 epsilon ((sigma/r)^12 - (sigma/r)^6) form.

On Wed, Sep 13, 2017 at 10:02 AM, Hossein Geraili wrote:
Dear Lammps users,
I found out that I should convert the r min in charmm22 force field which I obtained from article, but there is still a concern why the formula form in the article that I use have this difference:
{eps ij [(rmin ij/r ij)^12 -(rmin ij/r ij)^6] + q i q j/r ij=== this formula is in the article.
the correct formula for rmin at CHARMM22 force field is( a 2 is missing):
eps ij [(rmin ij/r ij)^12 - 2*(rmin ij/r ij)^6].

So I am not sure that I should use this conversion:

1-rmin ij = (2)^1/6 *sig. ij

or because there is no two beside the second term, I should use another conversion(what?).

Excuse me for several messages, the previous messages were not clear, and I am sorry for that.

Thanks

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On Tue, Sep 12, 2017 at 10:31 PM, Hossein Geraili wrote:
Dear Lammps users,

I am using force field parameters of my molecule from an article which is using this formula for pair interaction potential:
{eps ij [(rmin ij/r ij)^12 -(rmin ij/r ij)^6] + q i q j/r ij}
but I know the correct formula for rmin is( a 2 is missing):
eps ij [(rmin ij/r ij)^12 - 2*(rmin ij/r ij)^6].
anyway, I should use pair_style lj/cut/coul/long for my system, which the VdW part is:
4*eps ij [(sig. ij/r ij)^12 - (sig. ij/r ij)^6].
and I know the relation between sig. and rmin:
rmin ij = (2)^1/6 *sig. ij
I wanted to ask, should I convert these to lammps, like converting rmin  to sig. and considering the changes( like 2, 4) and take them into account at inputting sig. and eps. values? or it is not necessary and lammps would consider rmin as sig.?
excuse me if it is obvious, but I cannot be sure which one is correct.
thanks in advance.

--
Hosein Geraili Daronkola
M.Sc.Graduated of physical chemistry
Physical Chemistry,
Department of Chemistry,
Sharif University of Technology.
geraili_hosein@...7110...

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--
Hosein Geraili Daronkola
M.Sc.Graduated of physical chemistry
Physical Chemistry,
Department of Chemistry,
Sharif University of Technology.
geraili_hosein@...7110...

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