Re: Iron Oxide and Arsenic

From: Axel Kohlmeyer (
Date: Sat Jun 11 2011 - 17:38:21 CDT

On Sat, Jun 11, 2011 at 6:25 PM, Salvador H-V <> wrote:
> Hi,
> Thanks Axel,
> It seems for me that I have only two options: Coarse-grained simulation with
> an effective potential or ab initio molecular dynamics.

all-atom simulations also use effective potentials.

> I was wondering if you could suggest a free software to performance
> ab-initio molecular dynamics.

there are several packages. all of them have strengths and weaknesses.
it is very difficult to recommend something. also, the question is whether
you can actually extract the information you want to find. you need a
significant chunk of compute power and still can only do 10s to 100s
of picoseconds at the most.

> I took a look in google and wikipedia, but to be sincere, I am lost with all
> the possible options!

you are looking in the wrong places. you have to search the literature
for people who have done something similar with compounds that
have similar properties. there is a large variety of empirical potentials
for inorganic materials, but you won't find them mentioned in webpages
related to "bio" simulations.

what i would expect to be the most likely way to do meaningful
simulations would be by generating your own parameter set
(not easy, though). the main question is whether you want to
simulate (nano)particles or solvated ions, how much the
two oxides would see each other and generally, what their
chemistry is. i would then start looking for publications of
similar simulations.


> I will really appreciate any help or suggestion.
> Thanks a lot,
> Salvador
> On Sat, Jun 11, 2011 at 5:16 PM, Axel Kohlmeyer <> wrote:
>> On Sat, Jun 11, 2011 at 6:09 PM, Salvador H-V <> wrote:
>> > Dear All,
>> >
>> > I was wondering if it is possible to simulate a mixture of arsenic and
>> > Iron
>> > Oxide in aqueous solution using classical molecular dynamics with NAMD.
>> > My main goal is to simulate absorption process, so  I am no interested
>> > in
>> > chemical reactions.
>> the big question is where to get force field parameters and
>> how accurate those have to be. chances are that you may
>> need an unusual functional form that require using tabulated
>> potentials or a code that has many different functional forms
>> available (NAMD does not).
>> cheers,
>>     axel.
>> > I have been trying to find information in the literature but without
>> > success.  I was wandering If somebody could point me out to an article o
>> > source for the methodology, it will be greatly appreciated!
>> >
>> > Thanks a lot,
>> >
>> > Salvador
>> >
>> >
>> >
>> >
>> --
>> Dr. Axel Kohlmeyer
>> Institute for Computational Molecular Science
>> Temple University, Philadelphia PA, USA.

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:20:25 CST