[gmx-users] Recommended parameters for NVE simulation of SPCE water

Michael Shirts michael.shirts at virginia.edu
Wed Aug 10 23:50:13 CEST 2011

> 1.  NOTE 1 above suggests that I use vdwtype = Shift.  When I do this, do
> you recommend that I apply long range dispersion corrections for both energy
> and pressure, using DispCorr = EnerPres, or for only energy, using DispCorr
> = Ener?  Typically, for various (non-NVE) calculations, I have been using
> DispCorr = no, but I am not sure if this is a good idea.  Pages 97-98 of the
> Gromacs 4.5.4 manual seem to suggest that the energy correction due to
> DispCorr is small and usually only significant for free energy calculations
> (which I will not be doing here).  As a rule of thumb, do you typically turn
> dispersion corrections off?

For constant pressure simulations, or for reaching the constant
pressure equilibrium simulation, you should definitely include a
dispersion correction -- the density will be too large, and will be
cutoff dependent.

For constant volume simulations, the dispersion correction will be
constant.  It will thus NOT affect energy conservation, but WILL
affect average potential energy and average total energy,

> 2.  NOTE 2 above suggests that I use either coulombtype = PME-Switch or
> coulombtype = Reaction-Field-zero.  Do you have any advice or
> recommendation?

For pretty good energy conservation, I would suggest:

rlist                           = 1.3
coulombtype              = PME
rcoulomb                    = 1.1
vdw-type                    = Switch
rvdw-switch                = 1.0
rvdw                          = 1.1

This should work quite well -- you might get some drift after 1-2 ns,
but not much.  I'm working on developing suggested PME parameters
right now for highly quantitative work, but it's not quite ready yet.

Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu

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