[gmx-users] rigid tetrahedral molecule

Fri Apr 29 21:05:57 CEST 2011

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.
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 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>:
>
>> 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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