[gmx-users] rigid tetrahedral molecule
Mark.Abraham at anu.edu.au
Thu Apr 28 08:00:42 CEST 2011
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
> 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).
> *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:
>> 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...
>> -- gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users