[gmx-users] rigid tetrahedral molecule
gyorgy.hantal at fc.up.pt
gyorgy.hantal at fc.up.pt
Fri Apr 29 19:15:51 CEST 2011
Citando David van der Spoel <spoel at xray.bmc.uu.se>:
> On 2011-04-29 17.55, 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.
Hmm, indeed, my average temperature differs slightly (0.068%) from the
prescribed value. So you mean only 3N - 12 d.o.f. can be
constrained..? This number seems insufficient to keep the molecule
rigid. I'll try with virtual sites.
Thanks for pulling my attention to this.
>> I hope this helps.
>> Citando Sanku M <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,
>>> 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>
>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> Sent: Wed, April 27, 2011 8:25:05 PM
>>> Subject: Re: [gmx-users] rigid tetrahedral molecule
>>> Sanku M wrote:
>>>> I am interested in simulating a anionic molecule BF4(-) ( Boron
>>>> tetrafluoride). In the paper which developed the parameters for this
>>>> 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
>>>> 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
>>> contact the authors who developed the model and ask how they did it.
>>> Then you
>>> know you're exactly reproducing what they did.
>>> -- ========================================
>>> 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
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> 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
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