[gmx-developers] External forces or field

[Gerrit Groenhof]

Can't it be that what you see is caused by the center of mass removal? 
also i
What happens if you try without the oscillating field, but the identical 
mdp parameters

Gerrit
S. Joseph wrote:
> Hi,
>
> I tried modifying  gromacs-4.03 to add  an external electric field
> that varies with time and space. I checked the mailing lists about
> adding external forces and there was an email from Gerrit Groenhoff
> who mentioned that external forces could be added in force.c.  I
> changed the function calc_f_el called by do_force in mdlib/sim_util.c.
> Instead of the Ext field used by gromacs, I added the force due to my
> external field using positions rvec x and time t. I assumed the
> positions were the actual positions (not shifted by PBC).  Now I am
> testing the system that has  a single Cl- ion with my external field
> acting on it with a cut-off (no PME) for electrostatics. I give it an
> initial velocity of 0.5 nm/ps in the conf.gro file used by grompp.
>
> If I have a frequency of oscillation of 100s of GHz of the field and
> from the field I gave I expect the ion trajectory to stabilize at a
> particular point based on theory. (This simulation was done and
> published by another person with NAMD). In my case I see this
> stabilization only if I give an extermely large timestep of (0.5-2
> ps). When I gave a timestep of 0.002 ps, depending on the magnitude of
> the field, the ion either did not move at all or moved in some
> trajectory which was radically different from expected (In NAMD after
> a time of 1 ns, it converged to a point even at a timestep of 2fs, but
> with GROMACS the time of convergence depended on my timestep- for
> larger timesteps-2ps, it converged within 1 ns, but smaller the time
> step, it took much longer - even microseconds until ultimately it
> stopped moving at the order of fs).
>
> Also g_energy does not give any kinetic energy for the ion. The
> results changed little whether I started from 0 velocity or 0.5 nm/ps
> velocity (That is, different temperatures did not give different
> results)
>
> Am I doing something wrong in adding forces or is the non neutrality
> of the system causing problems. At the beginning of calc_f_el, it is
> mentioned that the system has to be neutral for the correct virial,
> but I have an NVT system. I changed from single to double precision
> with no difference.
>
> I am planning to add water and other molecules to the system (NVT), so
> a timestep of 0.5ps would be unthinkable. Any ideas on what is going
> wrong?
>
> Regards,
> Joseph
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