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_(physics_and_chemistry)
<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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