[gmx-users] DNA-protein complex - which force field to use?

Paulo Netz paulo.netz at gmail.com
Mon Feb 2 09:50:00 CET 2015

Hi Jernej

I'll choose AMBER or CHARMM, because these two forcefields
have a more reliable description of nucleic acids. In my experience,
OPLS-aa and GROMOS do not seem to be able to produce stable
simulations in the large time scale for nucleic acids systems.

Best regards

Paulo Netz

2015-02-02 2:53 GMT+01:00 Jernej Zidar <jernej.zidar at gmail.com>:

> Hi everyone!
>   I would like to study a DNA-protein complex. The protein part is
> composed of aminoacids covalently attached to the DNA bases. Which
> force field would you recommend? Based on recent experience I was
> thinking of using either OPLS-aa or CHARMM. OPLS-aa would be the
> prefered choice because it performs way better than CHARMM.
>   Any recommendations or experiences?
> Thanks in advance!
> Jernej
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