Hi, On Wed, Feb 19, 2020 at 11:06 AM Robert Cordina <robert.cord...@strath.ac.uk> wrote:
> Dear Alessandra, > > Many thanks for your reply. > Re comment on nrexcl, I'm using nrexcl = 3 as the Sum paper states that > "In the NERD force field, atoms/sites within a molecule that do not > interact by any other intramolecular potential are also allowed to interact > though the Lennard-Jones potential". In the paper all bond stretching, > bond bending and torsion angle parameters are given, so is nrexcl = 3 > correct? LJ potentials are 1-4 interactions, so this looks the right way > to do it to me, but I stand to be corrected. > Re compressibility, that was a typo from my part in the email, it's > correctly set at 0.00001. > Re vdwtype, vdw-modifier, rvdw-switch, rvdw... I have read this section > multiple times but I'm still not sure how to translate the description in > the Sum paper to these settings. Any suggestions as to what "Interactions > were truncated and shifted at rc = 11 Å with energies shifted at this > distance" would mean for these settings? > > cutoff-scheme = Verlet > rcoulomb = 1.1 > coulombtype = Reaction-Field (I have to use this because I'm using the > epsilon-rf setting too right?) > epsilon-rf = a.bcd > > vdwtype = Cut-Off (?) > vdw-modifier = Potential-shift-Verlet or Potential-switch (?) > The sentence, you have reported, is not clear. It could be that the authors used vdwtype = cutoff vdw-modifier = Potential-shift (from mdp parameter of gromacs2020). rvdw = 1.1 But you should check with them, which treatment they use for the non-bonded interactions Best regards Alessandra rvdw-switch = 0 (?) > rvdw = 1.1 (will this just be the same as rcoulomb?) > > > Thanks again for your help. > > Best regards, > > Robert > > -----Original Message----- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf Of > Alessandra Villa > Sent: 19 February 2020 08:47 > To: gmx-us...@gromacs.org > Cc: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] Implementing the NERD Force Field in GROMACS > 2019.3 > > 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.cord...@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 > > -- > > 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-requ...@gromacs.org. > > > On Tue, Feb 18, 2020 at 3:13 PM Robert Cordina < > robert.cord...@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? 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