[gmx-users] lattice Coulomb energy between energy groups

[Justin A. Lemkul]

Gavin Melaugh wrote:
> Hi Justin
> 
> Thanks for the reply. I take it then, if I use the maxwarn option, it
> will still apply the exclusion for the short-range non-bonding interactions.
> 

Yes, that should work.  The error message is only there to prevent people from 
erroneously thinking they can exclude the PME mesh term.

-Justin

> Cheers
> 
> Justin A. Lemkul wrote:
>>
>> Gavin Melaugh wrote:
>>> Hi all
>>>
>>> I have set up a simulation with PBC using PME and specify an energy
>>> group enclusion involving some virtual sites and a hydrocarbon chain.
>>> i.e. hydrocarbon chain is one energy group and the virtual sites
>>> constitute the other group. Grompp generates the following warning
>>>
>>> "Can not exclude the lattice Coulomb energy between energy groups"
>>>
>>> I have checked the mailing list and the manual but there doesn't seem to
>>> be any concise answers. Given the fact that both groups are not charged
>>> is it O.K. to ignore this warning.
>>>
>> Probably.  The warning indicates that one cannot use energygrp_excl to
>> exclude components of the PME mesh; such exclusions only apply to
>> short-range interactions that can be decomposed pairwise.  Since the
>> PME mesh is dependent on all the entities in the system, there is not
>> way to simply calculate the mesh, except for some interactions between
>> groups A and B.  If there are no charges on groups A and B, you should
>> be fine.
>>
>> -Justin
>>
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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