[gmx-users] rigid tetrahedral molecule
Mark.Abraham at anu.edu.au
Thu Apr 28 06:14:34 CEST 2011
On 4/28/2011 1:54 PM, Sanku M wrote:
> 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
You should also do your homework about using LINCS and coupled triangles
of constraints, as I suggested last time.
> 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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