Thanks. The molecule was developed as a part of OPLS. The authors used a software called BOSS( developed in Bill Jorgensen's lab) . I guess this softwares have way to perform rigid body motion. There are other softwares like DL-POLY which can perform rigid body MD. So, I guess, in those cases, just declaring a molecule 'rigid' might be good enough. But, gromacs does not explicitly do rigid body MD. That's why I was looking for a trick .
________________________________ From: Justin A. Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Wed, April 27, 2011 8:25:05 PM Subject: Re: [gmx-users] rigid tetrahedral molecule Sanku M wrote: > Hi, > I am interested in simulating a anionic molecule BF4(-) ( Boron >tetrafluoride). In the paper which developed the parameters for this >molecule, >it is mentioned that it has been used as 'rigid' molecule i.e the molecule >only >has non-bonding interaction but there was no intramolecular motion as the >geometry was fixed. > I am trying to simulate this molecule in gromacs treating it as rigid. But, > I >was looking for best way to 'rigidify' this molecule. > > I was wondering whether using LINCS to constrain all B-F and F-F bonds will > be >good enough . Or, Should I use virtual sites ? If I really need to use >virtual >site, will it be something like TIP5P water model ? > Can someone suggest the best wayout ? > Constraints should do the trick, but probably the best approach is to simply contact the authors who developed the model and ask how they did it. Then you know you're exactly reproducing what they did. -Justin > Sanku > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
-- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
