[gmx-users] Fwd: FW: PME settings in free energy calculations
mrshirts at gmail.com
Thu Feb 4 14:48:31 CET 2016
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:
>> 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,
>> 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
>>> > 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
>>> 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,
>>> 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
>>> Gromacs Users mailing list
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> * 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-request at 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-request at gromacs.org.
More information about the gromacs.org_gmx-users