[gmx-users] Switch - Shift function electrostatics
Emanuel.Peter at chemie.uni-regensburg.de
Mon Jul 27 10:16:44 CEST 2009
At the moment I have a question which regards the different
electrostatic algorithms mentioned in the Gromacs-manual.
I did some simulations and I tried three different electrostatic
algorithms: Cut-off, Shift and PME.
It is clear to me what Shift and PME means principally, but I ask myself
which electrostatic algorithm is used by Cut-off.
I know that Cut-off means a twin-range-electrostatics calculation with
rlist as the first range and r_coulomb as the second range. Both are
calculated within different frequencies. Is that true ?
In my .log file it is mentioned that when using Cut-off a default value
r_coulombswitch equal to 0 is set. It is the same in the case of
Does that mean that I use in this special case a switch function which
switches at 0 nm which represents in this case a shift-function that
shifts my electrostatic potential in such a way, that it decays to zero
I think this means that I used a shift-function which is calculated
within the twin-range-electrostatics scheme.
Is this true?
What disadvantages does the twin-range-electrostatics calculation
have in comparison to PME?
Is it true that PME could stabilize my system artificially?
Now another question:
Some people who perform molecular-dynamics calculations are stabilizing
the dihedral angles in the forcefield to avoid 'unrealistical'
fluctuations of their protein. Is this a reasonable way to simulate a
Is it also reasonable to heat up a crystal -.pdb structure, determined
by x-ray, slowly from 50 K up to 300 K in a couple of steps?
Does this have any purpose or is this just a non proven setup of my
Thanks for your good advice in advance!
Institute of Phys. and Theor. Chemistry
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