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

Justin Lemkul jalemkul at vt.edu
Wed Feb 14 14:22:03 CET 2018

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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