[gmx-users] Switch - Shift function electrostatics

David van der Spoel spoel at xray.bmc.uu.se
Mon Jul 27 10:31:29 CEST 2009

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.
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.

> 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
> structure?
> Thanks for your good advice in advance!
> Best regards,
> Emanuel Peter
> Institute of Phys. and Theor. Chemistry
> 93053 Regensburg
> Germany
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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