[gmx-users] tabulated potentials - cutoff

Sabine Reisser sabine.reisser at kit.edu
Mon May 5 09:59:11 CEST 2014

So that means the electrostatics are calculated as given in the tables 
and no long range electrostatics corrections (like PME or RF) are applied?


Am 28.04.2014 18:28, schrieb 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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