[gmx-users] rigid tetrahedral molecule

Mark Abraham Mark.Abraham at anu.edu.au
Thu Apr 28 03:39:23 CEST 2011

On 4/28/2011 11:25 AM, Justin A. Lemkul wrote:
> 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.


Be aware that the coupled constraints make life tricky, and you should 
read up in the manual and literature for how best to use P-LINCS in such 
cases. Algorithms like SETTLE for rigid water exist for a reason...


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