[gmx-users] tabulated potentials - cutoff

Mark Abraham mark.j.abraham at gmail.com
Mon May 5 10:41:05 CEST 2014

On May 5, 2014 10:01 AM, "Sabine Reisser" <sabine.reisser at kit.edu> wrote:
> So that means the electrostatics are calculated as given in the tables
and no long range electrostatics corrections (like PME or RF) are applied?

Correct. The .mdp settings determine what interactions are computed; the
table just says the values computed. If you wanted PME long-range also,
there's a coulombtype for that.

> Cheers
> Sabine
> 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
>>> 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
>>> (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
>>> chains and opening a pore.
>>> This works. But I couldn't figure out how the long range interactions
>>> treated. I assumed only interactions are counted where the distance
>>> atoms is within the range defined in my tables. However, I do define a
>>> 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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