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 <mrshi...@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.vanromp...@uantwerpen.be> > Date: Wednesday, February 3, 2016 at 12:34 PM > To: Michael Shirts <michael.shi...@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.shi...@colorado.edu > Phone: (303) 735-7860 > Office: JSCBB D317 > Department of Chemical and Biological Engineering > University of Colorado Boulder > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.