[gmx-users] (Implicit Solvation) Effect of van der waal radii on dynamics of ion

[nichith]

I am trying to run a simulation of single Na ion in implicit solvent(water),
with OPLSAA FF in gromacs 4.5.7.
In particular I want to find the effect of the gbr parameter in the gbsa.itp
file in /gromacs-4.5.7d/share/gromacs/top/oplsaa.ff. 

[ implicit_genborn_params ]

; atype    sar    st    pi           gbr        hct
opls_102   0.16   1     1.215    0.1625   0.79 ; N (RNH3+)
opls_135   0.2     1     0.880    0.190    0.72 ; CB
opls_136   0.19   1     1.045    0.190    0.72 ; CB


I tried to run a simulation with three different values for the gbr
parameter. After the mdrun I find that the trajectory remains the same for
all three cases. So what exactly is the effect of this parameter on the
dynamics in implicit solvent method? Or am I missing something?

Any help is much appreciated.

Nichith
---------------------

.mdp file : 

integrator       = sd 
nsteps           = 1000000 
dt                 = 0.002 

implicit_solvent = GBSA 
gb_algorithm     = Still 
gb_epsilon_solvent = 80 

comm_mode     = none
pbc                = no 
nstlist             = 0 
ns_type          = simple 
rlist                = 0 
rgbradii           = 0 
coulombtype    = Cut-off 
rcoulomb         = 0 
vdwtype          = Cut-off 
rvdw               = 0 
tcoupl             = v-rescale 
tc_grps           = system 
tau_t              = 0.1 
ref_t               = 300 

;energygrps      = Ion_chain_A Ion_chain_B 

gen_vel          = yes 
gen_temp       = 300 
ld_seed          = 10092
gen_seed       = 10092
nstxout          = 100 
nstvout          = 100 
nstxtcout        = 100 
nstenergy        = 100 





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