Re: [gmx-users] tabulated potentials - cutoff

[Sabine Reisser]

Thanks for pointing me to this, this could actually work.

Cheers
Sabine


Am 05.05.2014 16:05, schrieb Mark Abraham:

I've no idea whether PME-User (read its description!) and enerygrp-table
interact in a way useful to you, but it might. You were going to test
whether your implementation of your model was working correctly anyway,
right? ;-)

Mark


On Mon, May 5, 2014 at 1:25 PM, Sabine Reisser <sabine.reis...@kit.edu>wrote:

But I cannot have specific interactions between two groups and normal PME
for the rest, right?

Cheers
Sabine



Am 05.05.2014 10:41, schrieb Mark Abraham:

  On May 5, 2014 10:01 AM, "Sabine Reisser" <sabine.reis...@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.

Mark

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

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

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

==================================================

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