[gmx-users] rigid tetrahedral molecule
Sanku M
msanku65 at yahoo.com
Thu Apr 28 11:07:03 CEST 2011
Thanks Mark for your comment. But, as far as degrees of freedom is concerned, if
there is a tetrahedral molecule as I shown below with atom #1 ( B) being center
of the tetrahedron , if we had defined the molecules in terms of bonds and
angles ( in stead of constraints ), we would have 4 bonds ( 1-2,1-3,1-4,1-5 )
and 6 angles ( 2-1-3,2-1-4,2-1-5,3-1-4,3-1-5 , 4-1-5 )at 109.45 degrees , thus
total ( 4+6)=10 descriptors .
In that case, the simulation goes fine . But, then wonder, why, for constraints,
we can put only 9 descriptors .
Also, I have tried all possible combination to get 9 constraints, but , in each
case, gromacs crashes. However, defining 4 bonds and 6 angles using high
force-constant lets the simulation go fine. So, on a second thought, I wonder
whether defining 9 bond-constraints to get a stable tetrahedral molecule is at
all possible. Do I need to go for some sort of compromise, where 4 bonds
( 1-2,1-3,1-4,1-5 ) are defined as constraints and 6 angles with high
force-constant are defined to maintain tetrahedral nature ?
I am not sure what should be the best possible 9 constraints .
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
________________________________
From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Thu, April 28, 2011 1:00:42 AM
Subject: Re: [gmx-users] rigid tetrahedral molecule
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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