[gmx-users] GROMOS96 53A6 with extended Berger lipid parameters (Prasanna)

[Justin Lemkul]

On 2/13/18 5:08 AM, Prasanna Dr wrote:
> Hi all,
>
> The force field combination used in GROMOS96 53A6 with extended Berger
> lipids contains L-J interaction cross-terms between protein lipid atom
> types? If so how abnormally high L-J interactions are tackled?
>
> In my case, to prepare the topology of my system (which contains proteins
> and DPPC), I followed KALP15 in DPPC tutorial (version Gromacs 5.0 and
> above) of Justin A. Lemkul.  Does this tutorial answers my first question?
> Does I have employed force filed combination rules effectively?

Force field combination rules are only overridden when using a 
[nonbond_params] directive. If you find something abnormal that needs to 
be fixed, then you'd implement it there. Note that the tutorial is 
instructive in demonstrating how to set up such a system, but it is not 
the best possible force field model out there.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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