[gmx-users] rigid tetrahedral molecule

[Sanku M]

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 <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at 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 at 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-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110427/de552283/attachment.html>