[gmx-users] Parameters for -Si-Si- chains?

[Semen Esilevsky]

ThanksTsjerk, Google is definitely our best friend :) However, digging for parameters and testing the funny mixed force field is not justified in this case - the project is small as well as the amount of financing :) So, I whould be very grateful if somebody could point me to the ready-to-use -Si-Si- GROMACS topologies (if they exists of course).



----- Original Message ----
From: Tsjerk Wassenaar <tsjerkw at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Tuesday, June 23, 2009 11:22:39 AM
Subject: Re: [gmx-users] Parameters for -Si-Si- chains?

Hi Semen,

When confronted with Si-Si-Si and radicals in the same sentence, I
don't get comforted and definitely wouldn't characterize it as 'rather
simmple' ;)
There seem to be quite a number of publications referring to MD of
Si-Si systems though. Try googling a bit, or try Web of Science; gives
quite a number of hits which you could use to extract parameters.
However, do try to assess how reasonable the assumptions/calculations
in these papers are for determining the parameters.

Cheers,

Tsjerk

On Tue, Jun 23, 2009 at 9:51 AM, Semen Esilevsky<yesint4 at yahoo.com> wrote:
> Dear All,
> Our colleges asked me to do some rather simple MD of the organic-silicone
> compounds (-Si-Si-Si- backbone with organic radicals), but it appeared to be
> not so simple because of the force field. Does anybody know about parameters
> for such systems, which are adapted for GROMACS? I've only found -Si-O-
> -parameters in standard ffgmx, which is not what I need. OPLS also has no
> parameters for -Si-Si-Si- chains. Probably somebody know about other force
> fields from which it is possible to transfer missed parameters?
>
> Regards,
> Semen
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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