[gmx-users] PME or Reaction field suitable for Gromos forcefield ?
David van der Spoel
spoel at xray.bmc.uu.se
Thu Dec 23 07:27:52 CET 2010
On 2010-12-22 22.57, Sanku M wrote:
> Thanks David for the response. I was going through the supporting
> material of your paper to understand the methodology .
> For G96 forcefield, you wrote
>
> 'For the gromos96 simulations marked “cutoff ” a reaction field with
>
> ǫ = 54 was applied beyond a cutoff of14 Å, for the opls/aa “cutoff ”
> simulations a straight cut-off
>
> of14 Å was chosen, and for the charmm “cutoff ” simulations a shift
> function was used between
>
> 10 and 12 Å. In addition, simulations were carried out using Particle
> Mesh Ewald (PME) for the
>
> calculation of electrostatic interactions[10, 11].'
>
>
> I am wondering what does the statement ' marked cutoff a reaction field
> with epsilon 54 beyond a cutoff of 14 Angstrom' in terms of gromacs
> .mdp terminology ? Does it mean that you used reaction field as long
> range electrostatics for G96. But, I may have understood wrong because
> in the last line you again write, all simulations used 'PME'.. Does it
> mean that for G96 , the simulations were repeated with both reaction
> field and PME separately ?
yes.
you would just exchange PME for RF. That's all. There is an enormous of
literature about this, an our paper is one which shows that at least for
our examples, but I would like to a argue for any system with full
charges (rather than just dipoles like water), PME is much better than
anything else.
>
> For the reaction field, I have never used it before, so I was wondering
> if you can provide bit more details in 'mdout.mdp' terminolgy for
> general setup of simulation using G96 forcefield .
>
> For example, for my simulation using Gromos96, I was using following
> mdout.mdp using PME. I am not sure that is a suitable setup for gromos
> simulation or not . Also, if I wanted to use reaction field, what
> modification I should have made here in long-range electrostat part ?
>
>
>
>
> ; RUN CONTROL PARAMETERS
> integrator = md
> ; Start time and timestep in ps
> tinit = 0.0
> dt = 0.004
> nsteps = 40000000
> ; For exact run continuation or redoing part of a run
> init_step = 0
> ; mode for center of mass motion removal
> comm-mode = Linear
> ; number of steps for center of mass motion removal
> nstcomm = 1
> ; group(s) for center of mass motion removal
> comm-grps =
> ; NEIGHBORSEARCHING PARAMETERS
> ; nblist update frequency
> nstlist = 10
> ; ns algorithm (simple or grid)
> ns_type = grid
> ; Periodic boundary conditions: xyz (default), no (vacuum)
> ; or full (infinite systems only)
> pbc = xyz
> ; nblist cut-off
> rlist = 1.4
> domain-decomposition = no
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype = pme
> rcoulomb-switch = 0
> rcoulomb = 1.4
> ; Relative dielectric constant for the medium and the reaction field
> epsilon_r = 1
> epsilon_rf = 1
> ; Method for doing Van der Waals
> vdw-type = cut-off
> ; cut-off lengths
> ;rvdw-switch = 0.7
> rvdw = 1.4
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr = no
> ; Extension of the potential lookup tables beyond the cut-off
> table-extension = 1
> ; Seperate tables between energy group pairs
> energygrp_table =
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing = 0.12
> ; 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-6
> ewald_geometry = 3d
> epsilon_surface = 0
> optimize_fft = no
>
>
>
> ------------------------------------------------------------------------
> *From:* David van der Spoel <spoel at xray.bmc.uu.se>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Wed, December 22, 2010 2:31:35 PM
> *Subject:* Re: [gmx-users] PME or Reaction field suitable for Gromos
> forcefield ?
>
> On 2010-12-22 21.57, Sanku M wrote:
> >
> >
> > ------------------------------------------------------------------------
> > *From:* Sanku M <msanku65 at yahoo.com <mailto:msanku65 at yahoo.com>>
> > *To:* gmx-user at gromacs.org <mailto:gmx-user at gromacs.org>
> > *Sent:* Wed, December 22, 2010 1:06:09 PM
> > *Subject:* PME of Reaction field for Gromos forcefield ?
> >
> > Hi,
> > I was trying to use g53a5 gromos forcefield for my study of protein in
> > water . But, I found the original parameterization paper of gromos , in
> > general uses reaction field for considering long range electrostatics .
> > But, I was wondering among PME and reaction field , which one will be
> > more apprpriate . Does PME cause any artifact if used with Gromos
> > forcefield ?
> > Alternatively, if I can get a sample .mdp file for typical gromos
> > forcefield simulation, that will also be very helpful .
> > Sanku
> >
> >
> >
> Check out
> Oliver Lange, David van der Spoel and Bert de Groot: Scrutinizing
> Molecular Mechanics Force Fields on the Microsecond Timescale With NMR
> Data Biophys. J. 99 pp. 647-655 (2010)
>
> We find that all FF perform better with PME.
>
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>http://folding.bmc.uu.se
> --
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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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