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

[Mohsen Ramezanpour]

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 ...*