[gmx-users] tabulated potentials - cutoff

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