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 <[email protected]> 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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