[gmx-users] rigid tetrahedral molecule

Mark Abraham Mark.Abraham at anu.edu.au
Thu Apr 28 08:00:42 CEST 2011 

On 4/28/2011 3:49 PM, Sanku M wrote:
>  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 ?)

I think it's seven coupled triangles, but that's not a relevant way to 
think about it. You have 5 atoms, so 3N-6 means 9 degrees of freedom, so 
you need 9 independent descriptors of relative atomic positions, so 9 
constraints. You were trying 10 and 5.

Because those constraints form triangles, you may need to take care with 
LINCS to get a stable simulation. Read up on the details here, I don't 
remember them.

> 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.

Forget about SETTLE - it was just an example to illustrate that this is 
not easy to do right. There's a specialised algorithm for rigid water 
(with three coupled bond constraints) because it is fiddly to get such 
things right (and fast).

Mark

> ------------------------------------------------------------------------
> *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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