[gmx-users] 'the reciprocal space calculation will not necessarily cancel'

Floris Buelens floris_buelens at yahoo.com
Tue May 14 14:02:30 CEST 2013


I'm not clear on the meaning and implications of this warning message from grompp:

WARNING 1 [file ../md.mdp]:

  With coulomb soft core, the reciprocal space calculation will not
  necessarily cancel.  It may be necessary to decrease the reciprocal space
  energy, and increase the cutoff radius to get sufficiently close matches
  to energies with free energy turned off.

Can anybody help me understand this better? In what context are we talking about cancellation? Around a thermodynamic cycle, or in a more narrow sense? Why would we not see such a cancellation?

In my understanding, if we have an A state with a certain set of charges and a B state with another, the end states at lambda=0 and lambda=1 should match exactly what you would see if you evaluated the A and B states independently without using the free energy code. Soft core vdW or coulomb would only affect the shape of the pathway connecting them and not the end points. So I'm having trouble seeing what kind of cancellation we're relying upon.

Thanks in advance for any insights!

More information about the gromacs.org_gmx-users mailing list