[gmx-users] tabulated potentials - cutoff
sabine.reisser at kit.edu
Mon May 5 13:25:20 CEST 2014
But I cannot have specific interactions between two groups and normal
PME for the rest, right?
Am 05.05.2014 10:41, schrieb Mark Abraham:
> 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.
>> Am 28.04.2014 18:28, schrieb Justin Lemkul:
>>> On 4/28/14, 9:19 AM, Sabine Reisser wrote:
>>>> 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 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
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