From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Sun Oct 18 2009 - 22:59:08 CDT
Based on discussion here and analysis of the trajectory, i think the
- extremely strong electric field distorts membrane by making it thicker
- that results in appearance of holes in membrane though which ions
travel with minimal resistance
- due to periodic boundary condition in z-direction ions accelerate
more with time and hit harder on the box walls that are perpendicular
- constant pressure control algorithm detects high pressure on those
walls and tries to expand simulation box
With ten times smaller electric fields membrane is not distorted.
Did anyone performed simulations of a simple water box with ions under
electric field? This might give insights on what maximum values of
electric field are safe to use.
On Thu, Oct 15, 2009 at 12:15 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Thu, 2009-10-15 at 11:22 -0400, Roman Petrenko wrote:
>> Guys, thanks for replies,
>> 1) yes i wrap all
>> 2) why 2 fs is an aggressive timestep. i thought the larger the system
>> the more applicable is this timestep, because we don't care about high
>> frequency motion.
> first off, the physics of the system and the integrator don't
> care about what you care about. the larger the system, the larger
> the possible fluctuations (including velocities) within the system.
> what i suspect is that you may just accidentally have had some
> very large force(s) on some atom(s) and that then the integrator
> broke down. since you increased the additional force due to the
> external field by a factor of 10, that may have become a significant
> contribution and just enough to bring the system over the top.
> of course, this is just a speculation based on my experiences
> with simulations on driving electrolytes through nanopores
> with (strong) external fields some 10+ years back. i would
> assume that a membrane protein system is much more sensitive
> than the crude models that we were able to run in the (good?)
> old times. ;-)
> if you don't care about fast motions, you could fiddle with the
> settings of the langevin thermostat, i.e. add more friction
> to make fast movements slower and stabilize a larger time step.
>> 3) center of mass drifts a _little bit_; is it that bad taking into
>> account that box expands eventually to 5000 A and center of mass moved
>> mere 170 A; here is center of mass of the system from complete
> as soon as the system expands significantly your results are bogus,
> so it is useless to discuss the 170A (which would be horrible), but
> the rest looks not too bad. when working with external fields, the
> COM drift is always an iffy issue and has to be monitored carefully,
> since there is always a chance that you become a victim of the
> "flying icecube syndrom", i.e. the total system starts to drift,
> and then due to the impact of the termostat your system effectively
> cools down. this is, obviously, correlated with the strength of the
> external field. in a "normal" system without an external field and
> if it is reasonably well equilibrated system, the langevin thermostat
> in NAMD should take care that the drift, once removed, does not
> build up again.
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