Sanku M wrote:
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 .
For an example, see the CHCL3 definition in the Gromos96 53A6 force field.
-Justin
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.abra...@anu.edu.au>
*To:* Discussion list for GROMACS users <gmx-users@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.abra...@anu.edu.au>
*To:* Discussion list for GROMACS users <gmx-users@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.abra...@anu.edu.au>
*To:* Discussion list for GROMACS users <gmx-users@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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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