[gmx-users] rigid tetrahedral molecule

Sat Apr 30 12:14:08 CEST 2011

On 2011-04-30 00.38, Mark Abraham wrote:
> On 4/30/2011 5:05 AM, Sanku M wrote:
>> Hi David,
>> Actually, I had tried to use vsites to make this molecule rigid. I
>> read the manual section 4.7 as well. But, unfortunately, for a 5-site
>> tetrahedral geometry I was not able to figure out the right vsite type
>> I should use. So, I was wondering whether you can provide some input
>> on the details of how to use virtual sites for a tetrahedral molecule.
>> It would have been helpful.
>
> David suggested using vsites "as well" as the multiple-constraints
> approach, because the molecule needs to have its degrees of freedom
> artificially increased to compensate for the artificial decrease.
>
> A vsite could only work if there was some way to take four atoms for the
> force calculation, project them into one (say COM), do the MD update
> step on the COM, and project the update back out. I've no idea whether
> that's sound or can be implemented, however.
It is quite involved. You need to keep the total mass constant and the 
moments of inertia.

For instance for methane one could construct 4 mass-particles M on the 
C-H bonds which are connected by 6 constraints. Then you can construct 
the virtual positions of C and H based on those four masses. A "real" 
methane has 5x3 degrees of freedom. The above construction has 4 masses 
* 3 dof - 6 constraints = 6 degrees of freedom left. This would 
therefore yield a correct rigid model.

>
> Mark
>
>> Sanku
>>
>> ------------------------------------------------------------------------
>> *From:* David van der Spoel <spoel at xray.bmc.uu.se>
>> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
>> *Sent:* Fri, April 29, 2011 11:46:01 AM
>> *Subject:* Re: [gmx-users] rigid tetrahedral molecule
>>
>> On 2011-04-29 17.55, gyorgy.hantal at fc.up.pt
>> <mailto:gyorgy.hantal at fc.up.pt> wrote:
>> >
>> > Hi Sanku,
>> >
>> > I've read about your problem just now, I don't know if it's already
>> > solved but I had the same problem some weeks ago and I also had a lot of
>> > troubles. But, finally I managed to solve it so maybe my experiences can
>> > be helpful for you:
>> >
>> > I think you should use SHAKE instead of LINCS. The manual says somewhere
>> > that LINCS cannot be used when constraining triangles (i.e. angles) but
>> > SHAKE works fine. On the other hand, if you use SHAKE you must switch
>> > from domain decomposition to particle decomposition (if you run your
>> > simulations parallel) just by using -pd when you type mdrun ('domain
>> > decomposition = no' in the mdp file is not enough).
>> >
>> > Then you must add as many constraints as degrees of freedom you have, so
>> > 9 in your case. In my case it was 15 for the PF6 anion. Maybe it'll work
>> > with less than 9 but in my case I had to add 15 contraints. What I did
>> > was the following:
>> > First I constrained all P-F bonds then I constrained fictious F-F bonds
>> > that I thought would make the molecule rigid. But it wasn't enough. Then
>> > I added some more redundant F-F contraints (up to 15 in total) in a bit
>> > arbitrary way until I found the 'magic combination'.
>> > Now my simulations run perfectly.
>> >
>> Please note that if your rigid molecule has less than 6 degrees of
>> freedom your temperature will be incorrect!
>> You can achieve a solution with the right number of d.o.f. by using
>> vsites as well. How to do this is left as an exercise for the reader.
>>
>> > I hope this helps.
>> >
>> > best,
>> > Gyorgy
>> >
>> >
>> > Citando Sanku M <msanku65 at yahoo.com <mailto:msanku65 at yahoo.com>>:
>> >
>> >> Thanks. The molecule was developed as a part of OPLS. The authors
>> used a
>> >> software called BOSS( developed in Bill Jorgensen's lab) . I guess this
>> >> softwares have way to perform rigid body motion. There are other
>> >> softwares like
>> >> DL-POLY which can perform rigid body MD. So, I guess, in those cases,
>> >> just
>> >> declaring a molecule 'rigid' might be good enough.
>> >> But, gromacs does not explicitly do rigid body MD. That's why I was
>> >> looking for
>> >> a trick .
>> >>
>> >>
>> >>
>> >>
>> >> ________________________________
>> >> From: Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>> >> To: Discussion list for GROMACS users <gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>>
>> >> Sent: Wed, April 27, 2011 8:25:05 PM
>> >> Subject: Re: [gmx-users] rigid tetrahedral molecule
>> >>
>> >>
>> >>
>> >> 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.
>> >>
>> >> -Justin
>> >>
>> >>> Sanku
>> >>>
>> >>
>> >> -- ========================================
>> >>
>> >> Justin A. Lemkul
>> >> Ph.D. Candidate
>> >> ICTAS Doctoral Scholar
>> >> MILES-IGERT Trainee
>> >> Department of Biochemistry
>> >> Virginia Tech
>> >> Blacksburg, VA
>> >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> >>
>> >> ========================================
>> >> -- gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >> 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
>> >>
>> >
>> >
>> >
>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
>> spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>http://folding.bmc.uu.se
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> 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
>

-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se