[gmx-users] Gromos 53a6, .mdp parameters for reaction field
James Lord
jjamesgreen110 at gmail.com
Tue Aug 11 02:42:23 CEST 2015
Hi Mohsen,
I am struggling with the same problem would you mind if I ask you to send
me your .mdp file ?
Cheers
James
On Tue, Aug 11, 2015 at 4:00 AM, Mohsen Ramezanpour <
ramezanpour.mohsen at gmail.com> wrote:
> As an update,
>
> After reading the suggested links I tried two .mdp files which were
> suggested in discussions as solutions. Both worked without any problem on
> my system.
>
> 1) rlist/r(columb/vdw)=(1.4/1.4) , in fact the problem seems to be the
> "twin-range + RF"
> 2) I used "twin-range + RF" BUT I reduced the nstlist to 1, this also works
> for my system.
>
> Thanks for your comments.
> Cheers
> Mohsen
>
> On Tue, Jul 21, 2015 at 4:44 PM, Mohsen Ramezanpour <
> ramezanpour.mohsen at gmail.com> wrote:
>
> > 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 ...*
> >> > >> > --
> >> > >> > Gromacs Users mailing list
> >> > >> >
> >> > >> > * Please search the archive at
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> before
> >> > posting!
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> >> > >> >
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> >> or
> >> > >> > send a mail to gmx-users-request at gromacs.org.
> >> > >> --
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> >> > >
> >> > >
> >> > >
> >> > > --
> >> > > 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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> >
> >
> >
> > --
> > *Rewards work better than punishment ...*
> >
>
>
>
> --
> *Rewards work better than punishment ...*
> --
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>
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