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
========================================
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