[gmx-users] Fwd: FW: PME settings in free energy calculations
Dries Van Rompaey
dries.vanrompaey at gmail.com
Fri Feb 5 13:31:37 CET 2016
Hi,
The corresponding mdp output section is:
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
coulomb-modifier = Potential-shift-Verlet
rcoulomb-switch = 0
rcoulomb = 1.0
; Relative dielectric constant for the medium and the reaction field
epsilon-r = 1
epsilon-rf = 0
; Method for doing Van der Waals
vdwtype = cutoff
vdw-modifier = Potential-switch
; cut-off lengths
rvdw-switch = 0.9
rvdw = 1.0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; Separate tables between energy group pairs
energygrp-table =
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.08
; FFT grid size, when a value is 0 fourierspacing will be used
fourier-nx = 0
fourier-ny = 0
fourier-nz = 0
; EWALD/PME/PPPM parameters
pme_order = 6
ewald_rtol = 1e-06
ewald-rtol-lj = 0.001
lj-pme-comb-rule = Geometric
ewald-geometry = 3d
epsilon_surface = 0
I evaluated the energy with:
Verlet - settings above (with standard verlet-buffer-tolerance)
@ s0 legend "Coulomb-14"
@ s1 legend "Coulomb (SR)"
@ s2 legend "Coul. recip."
0.000000 -2221.295898 -546205.250000 9271.518555
Total - 539155.0273
Verlet - settings above - with verlet-buffer-tolerance -1
0.000000 -2221.295898 -546205.250000 9271.516602
Total -539155.029296
Group - settings above
@ s0 legend "Coulomb-14"
@ s1 legend "Coulomb (SR)"
@ s2 legend "Coul. recip."
0.000000 -2221.296387 -487993.593750 -48931.437500
Total -539146.3276
Verlet - 3 nm cutoffs, 2.9 vdwswitch, coulomb-modifier none
@ s0 legend "Coulomb-14"
@ s1 legend "Coulomb (SR)"
0.000000 -2221.295898 -774817.875000
Total -777039.1709
Group - 3 nm cutoffs, 2.9 vdwswitch, coulomb-modifier none
@ s0 legend "Coulomb-14"
@ s1 legend "Coulomb (SR)"
0.000000 -2221.296387 -553398.125000
Total -555619.4214
Thanks,
Dries
On 4 February 2016 at 14:48, Michael Shirts <mrshirts at gmail.com> wrote:
> Also, can you be more precise about the inconsistency in the outputs
> you are seeing (with numerical output from GROMACS and analysis code).
>
> On Thu, Feb 4, 2016 at 6:17 AM, Michael Shirts <mrshirts at gmail.com> wrote:
> > Hi, Dries-
> >
> > Can you print out what the corresponding section of mdout.mdp look like?
> >
> > Have you tried using the cutoffs above with group cutoffs, and seen
> > what the difference is?
> >
> > On Thu, Feb 4, 2016 at 4:59 AM, Dries Van Rompaey
> > <dries.vanrompaey at gmail.com> wrote:
> >> Hi,
> >>
> >> I'm using PME with the default Potential-Shift-Verlet modifier. If I'm
> >> interpreting the manual and comments on the mailinglist correctly, the
> >> settings for rcoulomb-switch shouldn't affect this and PME-switching
> >> shouldn't be necessary (although there seems to have been some
> discussion
> >> about this, https://gerrit.gromacs.org/#/c/2220/). Has a consensus been
> >> reached elsewhere?
> >>
> >> Current nonbonded settings in my .mdp files are:
> >> ; Electrostatics
> >> coulombtype = PME
> >> rcoulomb = 1.0
> >>
> >> ; van der Waals
> >> vdwtype = cutoff
> >> vdw-modifier = Potential-switch
> >> rvdw-switch = 0.9
> >> rvdw = 1.0
> >>
> >> ; Apply long range dispersion corrections for Energy and Pressure
> >> DispCorr = EnerPres
> >>
> >> ; Spacing for the PME/PPPM FFT grid
> >> fourierspacing = 0.08
> >>
> >> ; EWALD/PME/PPPM parameters
> >> pme_order = 6
> >> ewald_rtol = 1e-06
> >> epsilon_surface = 0
> >>
> >> Thanks in advance,
> >>
> >> Dries
> >>
> >> On 4 February 2016 at 00:56, Michael Shirts <mrshirts at gmail.com> wrote:
> >>
> >>> Hi, Dries-
> >>>
> >>> Questions like this are probably best answered on the gmx-users list.
> >>> I can't say too much for the Verlet scheme -- I know that it was
> >>> relatively recently adapted for free energies, and there may be some
> >>> combinations of settings that could give unanticipated results.
> >>>
> >>> Pretty much all of our experience about nonbonded calculations and
> >>> free energies is collected in the following paper:
> >>> http://pubs.acs.org/doi/abs/10.1021/ct4005068. We used the group
> >>> cutoff scheme since that was the only one that was supported in
> >>> GROMACS at the time.
> >>>
> >>> Since you haven't sent any files, it's hard to tell what is actually
> >>> going on. The one thing that has a tendency to happen with the more
> >>> recent update schemes is if you set a potential modifier that is a
> >>> switch, but don't set the distance the switch starts at, then it is
> >>> automatically set to zero. Check the mdout.mdp to see if this is
> >>> happening.
> >>>
> >>> > From: Van Rompaey Dries <Dries.VanRompaey at uantwerpen.be>
> >>> Date: Wednesday, February 3, 2016 at 12:34 PM
> >>> To: Michael Shirts <michael.shirts at colorado.edu>
> >>> Subject: PME settings in free energy calculations
> >>>
> >>> Dear prof. Shirts,
> >>>
> >>> I'm currently trying to figure out the PME settings for a relative
> >>> free binding energy simulation I'm working on. I took the parameters
> >>> from Matteo Aldeghi's
> >>> paper(
> >>>
> http://pubs.rsc.org/en/content/articlelanding/2015/sc/c5sc02678d#!divAbstract
> >>> )
> >>> as a starting point (adapted for the Verlet scheme by scaling the
> >>> fourierspacing to 0.08 and setting coulomb = rvdw = 1.0). I then tried
> >>> to verify these settings by comparing a single point energy
> >>> calculation with these settings and one with very long coulomb cutoffs
> >>> as recommended on alchemistry.org.
> >>>
> >>> Unfortunately, I can't seem to get this quite right. I'm getting
> >>> differences in the hundreds of kj/mol, leading me to suspect I'm doing
> >>> something wrong. I'm calculating the energy values by extracting
> >>> CoulombSR and Coul-recip from the energy.xvg files. I've tried
> >>> calculating the energy with coulomb cutoffs at 3 nm and 10 nm, but
> >>> agreement with the PME results remains rather poor. David Mobley
> >>> mentioned you performed extensive research on this topic, and I'm
> >>> hoping you could point me in the right direction.
> >>>
> >>> Thanks in advance,
> >>>
> >>> Dries
> >>>
> >>>
> >>>
> >>> ~~~~~~~~~~~~~~~~
> >>> Michael Shirts
> >>> Associate Professor
> >>> michael.shirts at colorado.edu
> >>> Phone: (303) 735-7860
> >>> Office: JSCBB D317
> >>> Department of Chemical and Biological Engineering
> >>> University of Colorado Boulder
> >>> --
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