[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.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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