[gmx-users] Gromos 53a6, .mdp parameters for reaction field
Mohsen Ramezanpour
ramezanpour.mohsen at gmail.com
Tue Jul 21 21:52:32 CEST 2015
Hi Joao,
Thanks for comment, I am using 4.6.7 version.
On Tue, Jul 21, 2015 at 12:09 PM, João M. Damas <jmdamas at itqb.unl.pt> wrote:
> I have not looked thoroughly to your parameters, but which version of
> GROMACS are you using? Any version from 4.5.X onwards is known to be
> problematic with reaction field and twin-range (and I believe it has not
> been solved).
>
> It's hard to follow the entire conversation, but check here for part of it:
>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2011-November/005435.html
>
> João
>
> On Tue, Jul 21, 2015 at 6:44 PM, 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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