[gmx-users] rigid tetrahedral molecule

Justin A. Lemkul jalemkul at vt.edu
Thu Apr 28 03:25:05 CEST 2011

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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