[gmx-users] rigid tetrahedral molecule

Sanku M msanku65 at yahoo.com
Thu Apr 28 03:49:58 CEST 2011

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.


> Sanku

-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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