[gmx-users] rigid tetrahedral molecule

[Mark Abraham]

On 4/28/2011 1:54 PM, Sanku M wrote:
> Hi,
>   I tried to keep the geometry of the BF4 fixed by using constraints 
> using lincs. But , unfortunately, my simulation is crashing 
> immediately and if I try minimization with only 2 molecules, it 
> provides a lot of LINCS warning and generate a lot of step*.pdb file . 
> If I try to visualize the minimized snapshot in VMD, it looks like all 
> the distances I tried to constrain decreased drastically. Finally, 
> trying MD run with this "minimized" configuration results in crashing 
> due to bad contacts.
>
>  I am sure I am doing something wrong and it might be that my itp file 
> is wrong . So any help will be highly appreciated.
> Here is the details of what I did.
>
>       The geometry of the molecule is tetrahedral with B at the center 
> and 4 F atoms is surrounding it in a tetrahedral manner.
> I first generated a itp file for BF4 which is shown below: I first got 
> the LJ parameters and charges for B and F atom and put them in 
> ffoplsnb.itp file as new atom types opls_1014 and opls_1015 
> . Initially I tried to put contsraint along all bonds ( i.e among F 
> atoms as well ). But, grompp provides warning that number of 
> constraint is more than number of degrees of freedom. So, I reduced 
> number of constraints by only putting constraint among B and F. But, 
> it did not work either.

Sure, you need as many constraints as 
http://en.wikipedia.org/wiki/Degrees_of_freedom_(physics_and_chemistry) 
<http://en.wikipedia.org/wiki/Degrees_of_freedom_%28physics_and_chemistry%29>

You should also do your homework about using LINCS and coupled triangles 
of constraints, as I suggested last time.

Mark

> Here is  the .itp file I wrote for rigid BF4 . It will be great if 
> someone can point me what I am doing wrong.
>
>   [ moleculetype ]
> ; molname       nrexcl
> BF4             3
>
> [ atoms ]
> #ifdef _FF_OPLS
>      1  opls_1014   1    BF4    B       1      0.8276
>      2  opls_1015   1    BF4    F1      1      -0.4569
>      3  opls_1015   1    BF4    F2      1      -0.4569
>      4  opls_1015   1    BF4    F3      1      -0.4569
>      5  opls_1015   1    BF4    F4      1      -0.4569
> #endif
> [ constraints ]
>   1  2   1   0.146
>   1  3   1   0.146
>   1  4   1   0.146
>   1  5   1   0.146
>   ;  2  3   1   0.238
> ;  2  4   1   0.238
> ;  2  5   1   0.238
> ;  3  4   1   0.238
> ;  3  5   1   0.238
> ;  4  5   1   0.238
>
> [ exclusions ]
> 1       2       3    4  5
> 2       1       3    4  5
> 3       1       2    4  5
> 4       1       2    3  5
> 5       1       2    3  4
>
>
> ------------------------------------------------------------------------
> *From:* Mark Abraham <Mark.Abraham at anu.edu.au>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Wed, April 27, 2011 8:39:23 PM
> *Subject:* Re: [gmx-users] rigid tetrahedral molecule
>
> 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.
>
> Yep.
>
> 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...
>
> Mark
>
>
>
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