[gmx-users] Switch - Shift function electrostatics

Ran Friedman r.friedman at bioc.uzh.ch
Mon Jul 27 11:16:30 CEST 2009

David van der Spoel wrote:
> Emanuel Peter wrote:
>> Dear Gromacs-users,
>> 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
>> r_vdwswitch.
>> 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
>> at r_coulomb?
>> 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?
> No, it is the other way around. Cut-offs are bad.
> Check:
> J. Chem. Theor. Comp. 2 pp. 1-11 (2006)
>> 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
>> protein?
> No, you are changing the force field in that way. I haven't heard of
> this previously.
I guess you mean CMAP in CHARMM.
You can check out the relevant paper, which also includes details about
some other force fields.


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