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

[Florian Dommert]

* Semen Esilevsky <yesint4 at yahoo.com> [2009-06-23 06:06:58 -0700]:

>
>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).

Mixing force field parameters is very dangerous, because they are
parametrized in respect to each other, therefore I am quite sure that
Tserk did not meant that you should mix any parameters. The choice of a
suitable set of parameters depends on many factors, the environment you
simulate, the boundary conditions, temperature ... . So I interpret
Tsjerks reply in the following way: literature should be searched to find a reference
article describing the simulation of a very similar system, from this
reference a consistent force field should derived and applied in your
simulation.

Flo

>
>
>
>----- 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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-- 
Florian Dommert
Dipl.-Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

Tel: +49 - 711 / 6856-3613
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EMail: dommert at icp.uni-stuttgart.de
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