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

[Mark Abraham]

On Tue, Feb 25, 2014 at 9:41 AM, nichith <nichith at gmail.com> wrote:

> 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?
>

With a single ion, the only thing you can observe is the energy, right?
Does that differ? If not, then there's a problem. You may not be sourcing
the correct .itp file when you re-run grompp (e.g. check by making a
deliberate syntax error). Or there may be a code problem (don't think this
was a fix any time, but you could try with 4.6.5).



> 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
>

As grompp should be warning you, this is generally not good practice in
these kinds of simulations. Angular is better, IIRC. Here, all you are
probably observing in the trajectory is the propagation of the velocity,
since there can be no force.

Mark


> 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
>
>
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/Implicit-Solvation-Effect-of-van-der-waal-radii-on-dynamics-of-ion-tp5014788.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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