[gmx-users] Error note

Justin A. Lemkul jalemkul at vt.edu
Thu Feb 23 15:45:36 CET 2012

Gavin Melaugh wrote:
> I am using 4.5.5

The warning is only triggered if the charge group is 10 atoms or larger.  Why 
this is the threshold, I can't say.  I didn't write the code ;)

You may still want to do some tests with smaller charge groups to make sure the 
changes do not produce significantly different energies.


> Justin A. Lemkul wrote:
>> Gavin Melaugh wrote:
>>> Hi Justin
>>> I saw this and had a question.
>>> How important is it for a charge group to be neutral?
>> It isn't.  Conventional use dictates that the charge group bear an
>> integral charge.  With PME, this is not necessary.  Many force fields
>> do not use charge groups at all (i.e., single-atom charge groups).
>>> In one of my systems I model a solvent of crown ethers using an all atom
>>> model. The smallest neutral unit comprises a CH2-O-CH2 (7 atoms). I have
>>> used this as a charge group to and get no warnings.
>> The only implication I can think of would be in neighbor searching. 
>> If the group is large, then short-range forces may not be calculated
>> accurately.  The warning from grompp was a recent addition to the
>> code; if you're using an older version you may not have triggered it.
>> -Justin


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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