[gmx-users] rigid tetrahedral molecule

[Sanku M]

 I went through the LINCS manual .  But, I am still struggling with coming up 
with the idea of putting correct constraint to maintain the rigidity of 
tetrahedral molecule .  I seem to understand  from your suggestion that the 
tetrahedral can be seen as a combination of  4  coupled triangles.( or am I 
still wrong about it ?)
In that case, am I supposed to use multiple settle to keep the molecule in a 
tetrahedral fashion ? I am sorry but if you can explain it in bit more details, 
I might get the point.



________________________________
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 11:14:34 PM
Subject: Re: [gmx-users] rigid tetrahedral molecule

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_%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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