[gmx-users] Fwd: FW: PME settings in free energy calculations

[Michael Shirts]

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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