[gmx-users] Error in energy group exclusion

[Justin A. Lemkul]

bipin singh wrote:
> Thanks for your reply,
> Yes, you are correct, I want calculate the non-bonded interaction
> energies terms for
> Protein-Protein and Protein-Solvent system using rerun of the
> trajectory from a already finished simulation
> (using PME method).Please suggest whether there is any way to get these terms.
> 

You can obtain short-range nonbonded energies between the desired energy groups 
using the method you proposed.  grompp is just warning you that you cannot 
exclude all terms when using PME; it's a helpful hint in case someone wants to 
try to run a simulation that they think has all terms excluded, which is not 
reality.  You can override the warning with -maxwarn, or change coulombtype to 
cutoff (in which case you'll probably get new warnings about cutoffs not being 
accurate, which also isn't relevant because this is a rerun of a presumably 
sound trajectory).

It's up to you to decide whether neglecting the long-range term in order to 
calculate short-range terms is useful.  The general consensus is that such 
energies, in absolute terms, don't mean anything, because you're neglecting an 
energy term (the PME mesh) that typically accounts for a (very) large fraction 
of the total Coulombic interactions in the simulated system.

-Justin

> On Mon, May 23, 2011 at 23:06, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>> 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
>>
>> ========================================
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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

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