[gmx-users] Gromos 53a6, .mdp parameters for reaction field
Mohsen Ramezanpour
ramezanpour.mohsen at gmail.com
Wed Jul 22 00:44:26 CEST 2015
I looked at the first link, it was a useful discussion.
Now, I am trying suggestions with rlist/r(columb/vdw)=(1.4/1.4) and
everything is working properly till now.
It seems the problem was the "twin-range" + RF with this version of Gromacs
as has been discussed and you mentioned already.
I am playing a little bit to see if I everything will be fine with the rest
of test simulation.
I will reply again after my tests.
Thanks for the links
Cheers
Mohsen
On Tue, Jul 21, 2015 at 4:21 PM, João M. Damas <jmdamas at itqb.unl.pt> wrote:
> 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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>
>
> --
> João M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
> Tel:+351-214469613
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