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 <sp...@xray.bmc.uu.se>
*To:* Discussion list for GROMACS users <gmx-users@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.han...@fc.up.pt
<mailto:gyorgy.han...@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 <msank...@yahoo.com <mailto:msank...@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 <jalem...@vt.edu <mailto:jalem...@vt.edu>>
>> To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@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
>>
>> ========================================
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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.
sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>http://folding.bmc.uu.se
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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