[gmx-users] Implementation of time-dependent Electric Field

[Viswanadham Sridhara]

Thanks for the quick feedback!

On 5/10/06, Erik Lindahl <lindahl at sbc.su.se> wrote:
>
> Hi,
>
> On May 10, 2006, at 1:24 PM, David van der Spoel wrote:
>
> > Viswanadham Sridhara wrote:
> >> Hi everyone,
> >> This is regarding implementation of time-dependent electric field
> >> on the system.
> >> I tried looking into the manual, and did a bit of survey in
> >> mailing lists. I still dont know how to implement E_zt in .mdp
> >> options.
> >> As an example, can anyone tell me how to implement a 5ns E (V/nm)
> >> trapezoidal pulse (1ns rise and fall times with 3ns pulse on time).
> > you can't.
> >
> > please check the source code, src/mdlib/sim_util.c
>
> To clarify - the routine in question is called calc_f_el() and is
> _extremely_ simple, so you can probably implement it yourself with
> very little extra work.
>
> The coordinates of particule i (counting starts from 0, since we're
> using C) are available in units of nm in
>
> x[i][XX]
> x[i][YY]
> x[i][ZZ]
>
> Similarly, the forces you want to alter are in units of kJ/mol/nm, in
>
> f[i][XX]
> f[i][YY]
> f[i][ZZ]
>
> ... and the particle charge is charge[i], in electron charge units.
>
> So, go through all particles, check e.g. the z-coordinate and assign
> a field in V/nm based on this. We need to convert it to MD units too,
> so the force correction will be
>
> f[i][ZZ] += your_calculated_field_at_this_z_coordiate * FIELDFAC *
> charge[i].
>
>
>
> Cheers,
>
> Erik
>
>
>
>
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--
Viswanadham Sridhara,
Graduate Research Assistant,
Old Dominion University,
Norfolk, VA-23529.
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