[gmx-users] Implementing the NERD Force Field in GROMACS 2019.3

[Alessandra Villa]

HI,

Below some suggestions assuming that the energy terms are correctly
implemented (force field)

On Tue, Feb 18, 2020 at 3:13 PM Robert Cordina <robert.cordina at strath.ac.uk>
wrote:

> Hi, I’m trying to use the NERD forcefield (Sum et al. J. Phys. Chem. B
> 2003, 107, 14443-14451) in GROMACS 2019.3 for a pure triacylglyceride
> system, however I’m not entirely sure that I’m setting up the equilibration
> parameters in the mdp file correctly as I’m getting different simulation
> results from others who have published papers using this force field.  All
> the bonding and non-bonding interactions have been typed up in the
> respective force-field files, and assuming those are correct (I’ve checked
> and re-checked them multiple times), the only thing I can think that is not
> correct are the mdp parameters.
>
> The Sum et al. paper, and another paper (Pizzirusso et al.
> J.Am.Chem.Soc.2018, 140, 12405−12414) state the following (text from Sum
> paper in italics, text from Pizzirusso paper in bold, what I’ve put in the
> mdp file in regular font)
>
> Both NVT and NPT calculations were performed using 40 molecules in a cubic
> box with periodic boundary conditions
> pbc                         = xyz
>
>
If you do not have a pre-built structure, your equilibration time may be
longer that in the original paper, the best is to ask the authors the
coordinate of pre-equilibrated system.



> Interactions were truncated and shifted at rc = 11 Å with energies shifted
> at this distance
> rcoulomb             = 1.1 (am I missing something here?)
>
>
here you miss the vdwtype; vdw-modifier; rvdw-switch¶; rvdw

(see for definition:
http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=vdw#Van
)



> The system evolved with a leapfrog algorithm using a 2 fs timestep
> integrator            = md
> dt                            = 0.002
>
> Constant temperature and constant pressure simulations were maintained
> with the Berendsen’s thermostat and barostat, respectively, by uniform
> scaling of the atomic velocities (temperature) and by uniform scaling of
> the atomic positions and box length (pressure)
> Atomistic MD was performed using GROMACS 4.5 under an NPT ensemble. In
> this ensemble, temperature and pressure were kept constant using a
> Berendsen thermostat/barostat.  Temperature and pressure couplings of 1 and
> 10 ps were used, respectively. Compressibility was fixed at 1 × 10-5 bar-1,
> and anisotropic pressure coupling was used in the MD simulations.
> tcoupl                   = Berendsen
> tau-t                      = 1.0
> tc-grps                  = XXX
>

system

> ref-t                       = 350
>
> pcoupl                  = Berendsen
> pcoupltype         = anisotropic
> compressibility  = 0.0001 0.0001 0.0001 0.0001 0.0001 0.0001
>

compressibility is   10-5 bar-1

tau-p                     = 10
> ref-p                      = 1.01325 1.01325 1.01325 1.01325 1.01325
> 1.01325
>
> For all the calculations, a reaction-field correction was applied with
> continuum dielectric εRF to correct for long-range interactions due to
> electrostatics
> cutoff-scheme  = Verlet
> coulombtype     = Reaction-Field
> epsilon-rf            = a.bcd (I used actual numbers here of course)
>
>
> In addition I am using
> gen-vel                 = yes
> gen-temp            = 350
> gen-seed             = -1
> continuation      = no
>
>
> Should I be adding anything with respect to vdw?
>
>
> In the forcefield.itp file I’m setting the following
> nbfunc                  = 1
> comb-rule           = 2 (Sum paper states that they use Lorentz-Berthelot
> combining rule for the LJ parameters)
> gen-pairs             = yes
> fudgeLJ                = 1
> fudgeQQ             = 1
>
>
check that  nrexcl in topol.top is in line with the force field.


> In ffbonded.itp
> bondtypes func = 1
> angletypes func = 1
> dihedraltypes func = 5
>
>
>
Best regards
Alessandra



>
> Thanks in advance for your help.
>
> Robert
> --
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On Tue, Feb 18, 2020 at 3:13 PM Robert Cordina <robert.cordina at strath.ac.uk>
wrote:

> Hi, I’m trying to use the NERD forcefield (Sum et al. J. Phys. Chem. B
> 2003, 107, 14443-14451) in GROMACS 2019.3 for a pure triacylglyceride
> system, however I’m not entirely sure that I’m setting up the equilibration
> parameters in the mdp file correctly as I’m getting different simulation
> results from others who have published papers using this force field.  All
> the bonding and non-bonding interactions have been typed up in the
> respective force-field files, and assuming those are correct (I’ve checked
> and re-checked them multiple times), the only thing I can think that is not
> correct are the mdp parameters.
>
> The Sum et al. paper, and another paper (Pizzirusso et al.
> J.Am.Chem.Soc.2018, 140, 12405−12414) state the following (text from Sum
> paper in italics, text from Pizzirusso paper in bold, what I’ve put in the
> mdp file in regular font)
>
> Both NVT and NPT calculations were performed using 40 molecules in a cubic
> box with periodic boundary conditions
> pbc                         = xyz
>
> Interactions were truncated and shifted at rc = 11 Å with energies shifted
> at this distance
> rcoulomb             = 1.1 (am I missing something here?)
>
> The system evolved with a leapfrog algorithm using a 2 fs timestep
> integrator            = md
> dt                            = 0.002
>
> Constant temperature and constant pressure simulations were maintained
> with the Berendsen’s thermostat and barostat, respectively, by uniform
> scaling of the atomic velocities (temperature) and by uniform scaling of
> the atomic positions and box length (pressure)
> Atomistic MD was performed using GROMACS 4.5 under an NPT ensemble. In
> this ensemble, temperature and pressure were kept constant using a
> Berendsen thermostat/barostat.  Temperature and pressure couplings of 1 and
> 10 ps were used, respectively. Compressibility was fixed at 1 × 10-5 bar-1,
> and anisotropic pressure coupling was used in the MD simulations.
> tcoupl                   = Berendsen
> tau-t                      = 1.0
> tc-grps                  = XXX
> ref-t                       = 350
>
> pcoupl                  = Berendsen
> pcoupltype         = anisotropic
> compressibility  = 0.0001 0.0001 0.0001 0.0001 0.0001 0.0001
> tau-p                     = 10
> ref-p                      = 1.01325 1.01325 1.01325 1.01325 1.01325
> 1.01325
>
> For all the calculations, a reaction-field correction was applied with
> continuum dielectric εRF to correct for long-range interactions due to
> electrostatics
> cutoff-scheme  = Verlet
> coulombtype     = Reaction-Field
> epsilon-rf            = a.bcd (I used actual numbers here of course)
>
>
> In addition I am using
> gen-vel                 = yes
> gen-temp            = 350
> gen-seed             = -1
> continuation      = no
>
>
> Should I be adding anything with respect to vdw?
>
>
> In the forcefield.itp file I’m setting the following
> nbfunc                  = 1
> comb-rule           = 2 (Sum paper states that they use Lorentz-Berthelot
> combining rule for the LJ parameters)
> gen-pairs             = yes
> fudgeLJ                = 1
> fudgeQQ             = 1
>
> In ffbonded.itp
> bondtypes func = 1
> angletypes func = 1
> dihedraltypes func = 5
>
>
>
> Thanks in advance for your help.
>
> Robert
> --
> 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.