[gmx-users] Error in energy group exclusion

[Justin A. Lemkul]

bipin singh wrote:
> Thanks for your reply,
> I have already done with the final simulation, and now if I have to
> change the method for electrostatic calculation(instead of PME)
> for energy group exclusion, then will it make sense i.e. how
> consistent it would be with my simulation results(with PME).
> Please suggest......
> 

I'm not 100% clear on what you're doing, but I assume you're trying to do some 
rerun of a trajectory to calculate various energy components?  If that's the 
case, there is a wealth of discussion on this topic in the list archive.  It is 
generally an exercise in futility or ambiguity.  If a trajectory was generated 
using long-range methods like PME, what sense is it to re-calculate some 
component of the the energies of configurations that were created using a 
different method?  The long-range terms may have a significant impact on the 
dynamical behavior, which you're now ignoring.

If this is not your intent, then please explain further.

-Justin

> On Mon, May 23, 2011 at 21:28, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>> bipin singh wrote:
>>> Hello users,
>>> I am getting the following warning during the grompp
>>>
>>> ---------------------------------------------------------------------------------
>>> WARNING 1 [file md.mdp]:
>>>  Can not exclude the lattice Coulomb energy between energy groups
>>>
>>> -----------------------------------------------------------------------------------
>>>
>>> I am providing the following energy groups and  energy exclusion group
>>> in my mdp file
>>> energygrps=Protein SOL
>>> energygrp_excl=Protein Protein SOL SOL
>>>
>>> Please suggest me, why I am getting the above error and how to get rid
>>> of this error.
>>>
>> Presumably you're using PME for long-range electrostatics.  The message
>> you're getting is grompp trying to help you realize that with PME it is not
>> possible to completely exclude all energetic terms, since the long-range
>> mesh is always calculated.  Only short-range nonbonded interactions (LJ and
>> Coulombic terms) are excluded in the mechanism above.
>>
>> -Justin
>>
>> --
>> ========================================
>>
>> 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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> 
> 
> 

-- 
========================================

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

========================================