[gmx-users] rigid tetrahedral molecule

[David van der Spoel]

On 2011-04-29 19.15, gyorgy.hantal at fc.up.pt wrote:
> 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.
> Gyorgy
It is worse than this. If you have e.g. 4 degrees of freedom left after 
subtracting the constraints the temperature will be computed as
(Ndf/2) kB T = Ekin
in that case your T will be 6/4 of what it should be, so if you couple 
to 200 K, mdrun will print 200K, but the real T will be 300 K (or the 
other way around). mdrun prints the number of degrees of freedom to help 
you figure this out.

>
>
>>> I hope this helps.
>>>
>>> best,
>>> Gyorgy
>>>
>>>
>>> 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,
>>>> 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>
>>>> 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:
>>>>> 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 | (540) 231-9080
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>
>>>> ========================================
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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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>
>
>


-- 
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