[gmx-users] partial exclusion of interactions within 1-4

[Alex]

This is the part I don't really understand, as I've never done this 
before. Let's assume we generated those pairs (it would actually be easy 
to obtain directly from bonds/angles/dihedrals). LJ is set throughout 
the system. Can one specify pairs with specific LJ params only for those 
pairs? In other words, will the [pairs] section accept columns like 'i j 
sigma epsilon'?

Feel free to tell me to RTFM, I just wish it could come with an 
_approximate_ page number... :)

Thanks,

Alex


On 5/23/2018 2:59 AM, Mark Abraham wrote:
> Hi,
>
> I suggested that [pairs] with the LJ parameters specified as zero was a way
> to be non-simultaneous. That adds back the Coulomb you want.
>
> Mark
>
> On Wed, May 23, 2018 at 10:55 AM Alex <nedomacho at gmail.com> wrote:
>
>> It is my understanding that either [pairs] or [exclusions] affect LJ and
>> electrostatics simultaneously, please correct me if I'm wrong. Maybe
>> this just isn't meant to be, being a highly artificial setup
>> (nearest-neighbor electrostatics on, LJ off)... The idea for this comes
>> from authors who used LAMMPS, and that thing allows such tricks with ease.
>>
>> The setup is almost guaranteed to work for me without including these
>> interactions (just set nrexcl=3 and go home), but I am needlessly
>> hesitating. In addition, I am absolutely against LAMMPS in this
>> particular case -- my postdoc is using it heavily on the same machine
>> with the same GPUs and it's massively slower (I estimate 5-7 times for
>> identical system size) than Gromacs. I just can't have 20-30 ns as my
>> simulated time.
>>
>> Alex
>>
>>
>> On 5/22/2018 3:17 AM, Mark Abraham wrote:
>>> Hi,
>>>
>>> That sounds right, given the wording (which I just didn't remember right
>>> then). So now that we understand that nrexcl applies to all moleculetypes
>>> in the .top then we pick whichever of 1 or 3 is most convenient (probably
>>> 1) and add either manual [pairs] or manual [exclusions] to the
>> appropriate
>>> moleculetypes until it works how we want. In particular, the manual
>> [pairs]
>>> should be able to have LJ parameters specified that are zero when you
>> want
>>> that. nrexcl and fudge values are just sugar for common cases of these
>>> patterns.
>>>
>>> Mark
>>>
>>> On Tue, May 22, 2018, 09:57 Alex <nedomacho at gmail.com> wrote:
>>>
>>>> I feel like I am being tested, but it says what I thought I knew:
>>>> "defines the name of your molecule in this *.top and nrexcl = 3 stands
>>>> for excluding non-bonded interactions between atoms that are no further
>>>> than 3 bonds away."
>>>>
>>>> This to me suggests that all coulombic+LJ interactions will be removed
>>>> for neighbors closer than third. By setting nrexcl = 1, one would get
>>>> nearest-neighbor coulombic back, along with LJ. However, I still want
>>>> the LJ off. Does this make sense?
>>>>
>>>> Alex
>>>>
>>>>
>>>> On 5/22/2018 1:48 AM, Mark Abraham wrote:
>>>>> Hi,
>>>>>
>>>>> What does the documentation of nrexcl in the reference manual say?
>>>>>
>>>>> Mark
>>>>>
>>>>> On Tue, May 22, 2018, 08:51 Alex <nedomacho at gmail.com> wrote:
>>>>>
>>>>>> Okay, let me try to rephrase the question, because it seems that I am
>>>>>> definitely unable to make it work and noone's replied so far.
>>>>>>
>>>>>> I have a "molecule" (a periodic boron nitride sheet) and a stand-alone
>>>>>> itp file for it -- everything works, i.e. it's a stable, well-behaved
>>>>>> structure the way I set it up.
>>>>>>
>>>>>> Within that molecule (and nowhere else) I need Coulombic interactions
>>>>>> between closest neighbors, while all other non-bonded interactions
>>>>>> should obey an effective nrexcl = 3. Is this something that can be
>> done
>>>>>> in Gromacs?
>>>>>>
>>>>>> Thank you.
>>>>>>
>>>>>> Alex
>>>>>>
>>>>>>
>>>>>> On 5/16/2018 7:12 PM, Alex wrote:
>>>>>>> Hi all,
>>>>>>>
>>>>>>> I think I understand how it works, but to double-check... There's a
>>>>>>> paper describing a setup of intramolecular interactions for boron
>>>>>>> nitride (https://pubs.acs.org/doi/10.1021/acs.jpclett.7b03443), in
>>>>>>> which non-bonded interactions *within* 1-4 were set up in the
>>>>>>> following way: LJ is off, but all electrostatic interactions are on.
>>>>>>> This is to achieve a better representation of the phonon spectrum and
>>>>>>> in fact it appears physically correct.
>>>>>>>
>>>>>>> Does this mean setting nrexcl to 1 for the crystal topology and
>>>>>>> creating a table of nonbond_param between B and N with sigma and
>>>>>>> epsilon equal to 0?
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Alex
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