[gmx-users] Gromos 53a6, .mdp parameters for reaction field

[João M. Damas]

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