[gmx-users] tabulated potentials - cutoff

[Justin Lemkul]

On 4/28/14, 9:19 AM, Sabine Reisser wrote:
> Hi,
>
> I'm using tabulated potentials to create a hole in a membrane. I define three
> groups: 2 dummy-atoms, all hydrophobic lipid chains, and rest. For the
> interactions between the dummy atoms and the hydrophobic chains I define an
> exclusively repulsive potential. All other interactions are defined normally
> (Coulomb, 6-12 LJ potentials). The 2 dummy atoms are placed on top and below the
> lipid bilayer, directly over each other. Then I use the pull code to pull the
> two dummy-atoms towards each other, thereby repelling the hydrophobic lipid
> chains and opening a pore.
>
> This works. But I couldn't figure out how the long range interactions are
> treated. I assumed only interactions are counted where the distance between
> atoms is within the range defined in my tables. However, I do define a cutoff
> radius max(rcoulomb, rvdw), I will call it rcutoff now. In the tables, I have to
> define values up to rcutoff+1.
> Is this cutoff radius only to tell GROMACS to expect values up to rcutoff+1? So
> everything until rcutoff+1 is calculated explicitly after the tables and
> everything beyond is ignored?
>
> I'm asking because usually membranes are quite sensitive to these cutoff values.
> I would assume that I would see clear changes in e.g. the area per lipid if I
> simulated long enough.
>

The nonbonded cutoff is whatever you set it to in the .mdp file.  The 
table-extension value is for bookkeeping and neighbor searching purposes.  It 
doesn't change the way the short-range forces are calculated.

-Justin

--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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