On 5/10/06, Erik Lindahl <[EMAIL PROTECTED]> 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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