[gmx-users] Error in energy group exclusion

[bipin singh]

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.

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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-- 
-----------------------
Regards,
Bipin Singh