* Semen Esilevsky <yesi...@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 <tsje...@gmail.com> To: Discussion list for GROMACS users <gmx-users@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<yesi...@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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php-- 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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php_______________________________________________gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting!Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49 - 711 / 6856-3613 Fax: +49 - 711 / 6856-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert !! PGP-ENCODED emails preferred !!
pgplL6cK4Vijb.pgp
Description: PGP signature
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
