Re: Iron Oxide and Arsenic

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Jun 11 2011 - 17:53:28 CDT

On Sat, Jun 11, 2011 at 6:48 PM, felmerino_at_uchile.cl
<felmerino_at_uchile.cl> wrote:
> Hey,
>
> I guess that most people use either cpmd or cp2k for ab initio md.

but iron - like many transition elements - can be a "tricky" element for those.

axel.

>
>
>
> best
>
>
>
> Felipe
>
> ----Mensaje original----
> De: chava09hv_at_gmail.com
> Fecha: 11-jun-2011 18:25
> Para: <namd-l_at_ks.uiuc.edu>
> Asunto: Re: namd-l: Iron Oxide and Arsenic
>
> 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.
>
> I was wondering if you could suggest a free software to performance
> ab-initio molecular dynamics.
>
> I took a look in google and wikipedia, but to be sincere, I am lost with all
> the possible options!
>
> I will really appreciate any help or suggestion.
>
> Thanks a lot,
>
> Salvador
>
>
> On Sat, Jun 11, 2011 at 5:16 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> On Sat, Jun 11, 2011 at 6:09 PM, Salvador H-V <chava09hv_at_gmail.com> 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
>> akohlmey_at_gmail.com  http://goo.gl/1wk0
>>
>> Institute for Computational Molecular Science
>> Temple University, Philadelphia PA, USA.
>
>
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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