[gmx-users] correct rlist and Verlet scheme

Timofey Tyugashev tyugashev at niboch.nsc.ru
Mon Feb 15 12:16:45 CET 2016

I've studied the relevant sections of the manual, but I don't consider 
myself to be familiar enough with this field to successfully guess the 
right settings.

ff99sb-ildn is included in the gromacs distribution, so shouldn’t be 
there some recommended settings for it? Or else how was it tested to run 

For now I've settled on the following parameters (the following is 
copied from mdout.mdp):

; cut-off scheme (Verlet: particle based cut-offs, group: using charge 
cutoff-scheme            = Verlet
; nblist update frequency
nstlist                  = 40
; ns algorithm (simple or grid)
ns_type                  = grid
; Periodic boundary conditions: xyz, no, xy
pbc                      = xyz
periodic-molecules       = no
; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,
; a value of -1 means: use rlist
verlet-buffer-tolerance  = 0.005
; nblist cut-off
rlist                    = 1.0
; long-range cut-off for switched potentials
rlistlong                = 1.05
nstcalclr                = -1

; 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
vdw-type                 = Cut-off
vdw-modifier             = Potential-shift-Verlet
; cut-off lengths
rvdw-switch              = 0
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           = 0.16
; 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                = 4
ewald-rtol               = 1e-05
ewald-rtol-lj            = 0.001
lj-pme-comb-rule         = Geometric
ewald-geometry           = 3d
epsilon-surface          = 0

And this is what the paper on it says:

    Each system was equilibrated at 300 K and 1 atm with 2.4 ns of MD
    simulation in the NPT ensemble. Then, MD simulations were carried
    out in the NVT ensemble for 720 ns using the Nosé-Hoover thermostat
    with a relaxation time of 1 ps. All simulations were performed using
    the Desmond MD program^16
    <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970904/#b16> version and either the Amber ff99SB^7
    <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970904/#b7> or the
    modified Amber ff99SB force field described herein, which we have
    termed ff99SB-ILDN. All bonds involving hydrogen atoms were
    constrained with the SHAKE algorithm.^17
    <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970904/#b17> A cutoff
    of 10 Å was used for the Lennard-Jones interaction and the
    short-range electrostatic interactions. The smooth particle mesh
    Ewald method^18
    <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970904/#b18> with a
    32 × 32 × 32 grid and a fourth-order interpolation scheme was used
    to compute the long-range electrostatic interactions. The pairlists
    were updated every 10 fs with a cutoff of 10.5 Å. We used a
    multistep RESPA scheme^19
    <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970904/#b19> for the
    integration of the equations of motion with timesteps of 2.0, 2.0,
    and 6.0 fs for the bonded, short-range nonbonded, and long-range
    nonbonded interactions, respectively. To check for potential biases
    introduced by long-range interactions between peptides in periodic
    images, we repeated these simulations for four of the amino acids
    (Xaa: Ile, Leu, Asp, and Asn) using a larger box with side length 37
    Å. We found that the results of these control simulations were
    within error of those using the smaller box sizes.

12.02.2016 22:06, gromacs.org_gmx-users-request at maillist.sys.kth.se пишет:
> Message: 1
> Date: Fri, 12 Feb 2016 14:09:28 +0000
> From: Mark Abraham<mark.j.abraham at gmail.com>
> To:"gromacs.org_gmx-users at maillist.sys.kth.se"
> 	<gromacs.org_gmx-users at maillist.sys.kth.se>, 	"gmx-users at gromacs.org"
> 	<gmx-users at gromacs.org>
> Subject: Re: [gmx-users] correct rlist and Verlet scheme
> Message-ID:
> 	<CAMNuMAR1-sQgc4_tMWJtzv1UWy6+nKbwXaYZ2h+PAbA3Y-KjdQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> Hi,
> As Adam says, you want to understand the reason why the forcefield
> specifies the settings it does. For example, until at least AMBER 2003,
> their force field papers did not specify PME parameters more precisely than
> "x nm cutoff was used." If PME was used at all.;-)  So you can be guided
> also by the parameters reported by successful users of these forcefields,
> particularly those of the various force field and software authors.
> rlist is a free parameter so long as you choose it large enough to avoid
> missing a significant number of interactions over the lifetime of the list
> - but it affects performance strongly. rcoulomb can be varied for
> equivalent accuracy if matching changes occur to PME parameters. VDW
> parameters should generally follow the force field derivation precisely
> (but add long-range corrections for dispersion) - GROMACS will not change
> these. You should check out the background information in the reference
> manual, sections 3.4.2 and 3.17.5
> Mark
> On Fri, Feb 12, 2016 at 1:56 PM Hardy, Adam<ah259 at hw.ac.uk>  wrote:
>> >There are people more qualified than me to explain the fine details of
>> >this, but in brief:
>> >
>> >Verlet on it's own doesn't adjust rvdw or rcoloumb (rcoulomb may be
>> >adjusted if you rae using PME for the coulomb interactions), but by default
>> >it will adjust the neighbour list cut-off (rlist) to remain with a
>> >specified energy tolerance given by verlet-buffer-tolerance. You can
>> >overide this behaviour and manually set rlist by setting
>> >verlet-buffer-tolerance=-1. Whether you want to or not will depend on why
>> >the forcefield has specified that cut-off, it may well be to achieve the
>> >same purpose, which is to propely catch interactions between atoms which
>> >move in or out of the cut-off radii between rlist update steps.
>> >
>> >Adam
>> >
>> >________________________________________
>> >From:gromacs.org_gmx-users-bounces at maillist.sys.kth.se  <
>> >gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Timofey
>> >Tyugashev<tyugashev at niboch.nsc.ru>
>> >Sent: 12 February 2016 12:47
>> >To:gromacs.org_gmx-users at maillist.sys.kth.se
>> >Subject: [gmx-users] correct rlist and Verlet scheme
>> >
>> >I have trouble in correctly setting cut-offs with Verlet scheme to match
>> >force-field specific settings.
>> >It automatically adjusts cut-off and it looks like they change their
>> >values from ones recommended for the force field.
>> >Is there a way to correct it and set up them properly?
>> >
>> >The paper on FF lists 1.0 nm for short-range electrostatic and LJ
>> >interactions.
>> >The cut-off of pairlists is 1.05 nm.
>> >
>> >The forcefield is 99SB-ILDN and is present in GROMACS itself.
>> >--
>> >Gromacs Users mailing list
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