Re: Periodic boundary conditions in membrane simulation

Date: Mon Aug 31 2009 - 16:02:43 CDT

Thanks for the advice. I think I will go with using two

---- Original message ----
>Date: Mon, 31 Aug 2009 14:01:26 -0400
>From: Axel Kohlmeyer <>
>Subject: Re: namd-l: Periodic boundary conditions in membrane
>On Mon, 2009-08-31 at 11:56 -0500, wrote:
>thanks for posting an interesting question, and for spending
>some effort on researching your options before asking. we have
>too few people doing this, so let me commend you for this and
>suggest to others to follow your example.
>> I am planing on running a md simulation of a membrane. I want
>> different ion concentrations on different sides of the
>> membrane. My concern is that if I apply periodic boundary
>> conditions ions will be able to diffuse from the top of
>> simulation box to the bottom of the simulation box and I will
>> not have a difference in the concentration of the ions. I
>right. this is a valid concern.
>> thought that maybe I should create a wall with Tcl boundary
>> conditions, or use two membranes, instead of one. I searched
>using two double layers or membranes would be the clean solution,
>but also a computationally more demanding. if you can afford to
>run a reasonable size system at a proper simulation speed, this
>would be the best way to proceed. you can average over the two
>membranes in your analysis (after considering the symmetry) and
>don't lose too much time, unless the k-space part of the PME
>will be too time consuming.
>using a regular wall is not such a good idea, as it will
>create an additional potential drop at the surface that may
>interfere with you calculation, so you'd have to use a very
>large water slab. what might be worth considering, if you
>are constrained in computational resources would be a
>_reflecting_ wall (i.e. velocities get reversed if z is
>larger than a cutoff value) that would only act on the ions.
>but i would still be concerned of generating an artificial
>potential drop across that wall, also because the waters
>on the other side of the wall would still "see" the ions
>and thus be affected by it. so if you'd go for this option,
>it would be highly recommended to make some tests with
>a (small) bulk water/electrolyte system comparing to pure
>water/electrolyte and see how far the boundary effects
>would reach.
>> around and could not find anything that said periodic boundary
>> conditions should be different for membrane simulations. I
>> asked someone in my group and he said that I did not have to
>> worry about this, and all I needed to do was turn wrap off. I
>this is bad advice. that wrapping keyword only affects the
>_output_ of coordinates, for the calculation of interactions,
>coordinates are _always_ wrapped to comply to the minimum
>image conventions.
>> disagreed with this. Eventually we decided to ask the namd
>> mailing list. I would appreciate any advice on how to set up
>> the simulation. I would also like someone to confirm or deny
>> whether molecules can move from the top of the simulation box
>> to the bottom, if periodic boundary conditions are applied
>> regardless of whether wrap is on or off.
>see above. to reiterate the coordinate wrap option does
>not affect the physics of your system at all.
> axel.
>> Thanks,
>> Jouko
>Dr. Axel Kohlmeyer
>Research Associate Professor
>Institute for Computational Molecular Science
>College of Science and Technology
>Temple University, Philadelphia PA, USA.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:14 CST