[gmx-developers] External forces or field

[David van der Spoel]

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?
Did you use temperature coupling? In my experience the standard 
implemented Efield works as advertised (even though the input is 
slightly difficult), however if you modified the code you're on your 
own... Maybe you can explain the difference in some more detail showing 
the default code and your code side by side.

Could you please post the ref. to the paper that was done with NAMD?

> 
> Regards,
> Joseph
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se