[gmx-users] rigid tetrahedral molecule

Sanku M msanku65 at yahoo.com
Thu Apr 28 05:54:35 CEST 2011

  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. 

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
[ 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.


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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