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

[V.V.Chaban]

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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