[gmx-users] OPLS/AA support for DNA

[Alex]

Yeah, I agree with Justin, this is pretty half-baked. On the other hand, I
am not after conformational changes, ds-DNA simulations, or things of that
nature. The things I am interested in would be mostly affected by the
partial charges and vdW parameters, and all of those seem to be from
standard oplsaa.

Alex


On Thu, Mar 26, 2015 at 3:56 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/26/15 8:30 AM, Smith, Micholas D. wrote:
>
>> There was some work on OPLS-AA/L on nucleic acids back in version 3 of
>> GROMACS. The group that did the work has a website where they discuss the
>> nucleic parameters located at:
>>
>> http://rnp-group.genebee.msu.su/3d/ff.htm
>>
>> There are likely newer parameters out there for opls, but I haven't
>> looked very hard for them.
>>
>>
> Anyone heard of anything peer-reviewed?  I know I'm not convinced by 2-ns
> simulations :)
>
> -Justin
>
> --
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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