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 <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
