[gmx-users] Gromos 53a6, .mdp parameters for reaction field
João M. Damas
jmdamas at itqb.unl.pt
Wed Jul 22 00:22:06 CEST 2015
I really think you may be losing time with LINCS parameters. Look at these
links too:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-March/088108.html
http://redmine.gromacs.org/issues/1400
You use a twin-range, i.e. a rlist/r(coulomb/vdw) of 0.8/1.4, so I really
think that this may be the source of your problems. The links that I sent
you present solutions to your problem, but almost always at a computational
cost, i.e. slower simulations.
João
On Tue, Jul 21, 2015 at 9:34 PM, V.V.Chaban <vvchaban at gmail.com> wrote:
> Maybe indeed downgrade to an earlier version.
>
> I, for sure, successfully used reaction field with gromacs 3-3-3
> (imagine when it was).
>
> Professor Vitaly V. Chaban
>
>
>
>
> On Tue, Jul 21, 2015 at 4:49 PM, Mohsen Ramezanpour
> <ramezanpour.mohsen at gmail.com> wrote:
> > Hi Chaban,
> >
> > Me too, but I do not know why starting with the same initial structures
> and
> > also starting from equilibrated structures again cause LINCS problems in
> one
> > not in the other one.
> >
> > I have tried lincs-iter and lincs-order and also lincs allowable angle
> > deviations but LINCS error still exist. This is why I think there is
> > something wrong with other parameters, e.g. reaction field!
> > Sure, I will look at epsilon_r, thanks.
> >
> >
> > On Tue, Jul 21, 2015 at 11:44 AM, V.V.Chaban <vvchaban at gmail.com> wrote:
> >>
> >> I do not see much connection between bond constraints and treatment of
> >> electrostatics beyond the cut-off distance.
> >>
> >> There is also an "epsilon_r" keyword. I would investigate what exactly
> >> it means and whether it is used in the reaction field procedure.
> >>
> >> The "all-bonds" contraint often results in different problems. You
> >> will have to play with the relevant parameters, like lincs_order and
> >> allowable deviation.
> >>
> >>
> >>
> >>
> >>
> >>
> >> On Tue, Jul 21, 2015 at 2:28 PM, Mohsen Ramezanpour
> >> <ramezanpour.mohsen at gmail.com> wrote:
> >> > Dear Gromacs users,
> >> >
> >> > I am interested in simulation of lipid bilayers with Gromos96 53a6.
> >> > As I understood this force field has been parametrized with reaction
> >> > field
> >> > instead of pme.
> >> >
> >> > Based on literatures, I have the following .mdp parameters:
> >> > But I am not sure of those as my system has lots of LINCS warnings
> with
> >> > these parameters.
> >> >
> >> > integrator = md
> >> > tinit = 0
> >> > dt = 0.002
> >> > nsteps = 50000
> >> > nstcomm = 1
> >> > comm-grps =
> >> >
> >> >
> >> > nstxout = 0
> >> > nstvout = 0
> >> > nstfout = 0
> >> > nstenergy = 100
> >> > nstxtcout = 5000
> >> > xtc-precision = 1000
> >> > energygrps = system
> >> >
> >> > nstlist = 5
> >> > ns_type = grid
> >> > pbc = xyz
> >> > rlist = 0.8
> >> >
> >> > coulombtype = reaction_field
> >> > rcoulomb-switch = 0
> >> > rcoulomb = 1.4
> >> > epsilon_rf = 62
> >> > vdw-type = Cut-off
> >> > rvdw-switch = 0
> >> > rvdw = 1.4
> >> > DispCorr = no
> >> >
> >> >
> >> > tcoupl = v-rescale
> >> > tc_grps = lipid water_ion
> >> > tau_t = 0.1 0.1
> >> > ref_t = 353 353
> >> > Pcoupl = berendsen
> >> > pcoupltype = semiisotropic
> >> > tau_p = 1.0 1.0
> >> > compressibility = 4.6e-5 4.6e-5
> >> > ref_p = 1.0 1.0
> >> >
> >> >
> >> > gen_vel = yes
> >> > gen_temp = 353
> >> > gen_seed = 17352
> >> >
> >> > constraints = all-bonds
> >> > constraint-algorithm = Lincs
> >> > unconstrained-start = no
> >> > shake-tol = 1e-04
> >> > morse = no
> >> >
> >> >
> >> > Interestingly, when I use common Gromos parameters including pme, as
> >> > follows, I do not have any LINCS problem with my system.
> >> >
> >> > integrator = md
> >> > tinit = 0
> >> > dt = 0.002
> >> > nsteps = 50000
> >> > pbc = xyz
> >> > comm-mode = linear
> >> > nstcomm = 1
> >> > comm-grps = system
> >> >
> >> >
> >> > nstxout = 0
> >> > nstvout = 0
> >> > nstfout = 0
> >> > nstlist = 10
> >> > ns_type = grid
> >> > nstenergy = 100
> >> > nstxtcout = 5000
> >> > energygrps = system
> >> >
> >> >
> >> > coulombtype = pme
> >> > rcoulomb = 1.0
> >> > rlist = 1.0
> >> > vdw-type = cutoff
> >> > rvdw = 1.0
> >> > DispCorr = no
> >> > table-extension = 1
> >> >
> >> >
> >> > tcoupl = v-rescale
> >> > tc-grps = lipid water_ion
> >> > tau-t = 0.1 0.1
> >> > ref-t = 353 353
> >> > Pcoupl = berendsen
> >> > Pcoupltype = semiisotropic
> >> > ref-p = 1.0 1.0
> >> > tau-p = 1.0 1.0
> >> > compressibility = 4.5e-5 4.5e-5
> >> >
> >> >
> >> > constraints = all-bonds
> >> > constraint-algorithm = Lincs
> >> >
> >> >
> >> > gen_vel = yes
> >> > gen_temp = 353
> >> > gen_seed = -1
> >> >
> >> >
> >> > Since the initial structures are the same, I think my parameters for
> >> > reaction field one has problem. I have also tried shorter time steps
> >> > (even
> >> > 0.5 fs) and also started from different initial structures but the
> >> > problem
> >> > still exist.
> >> >
> >> > I searched the mailing list but I could not find my answer completely.
> >> > Please let me know if you have any idea about parameters or if you
> have
> >> > any
> >> > .mdp file for reaction field (Gromos 53a6).
> >> >
> >> > Cheers
> >> > Mohsen
> >> > --
> >> > *Rewards work better than punishment ...*
> >> > --
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> >
> >
> >
> > --
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> --
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--
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613
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