[gmx-users] Implementation of time-dependent Electric Field
muta.mestri at gmail.com
Wed May 10 16:02:19 CEST 2006
Thanks for the quick feedback!
On 5/10/06, Erik Lindahl <lindahl at sbc.su.se> wrote:
> 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
> Similarly, the forces you want to alter are in units of kJ/mol/nm, in
> ... 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 *
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Graduate Research Assistant,
Old Dominion University,
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