[gmx-users] rigid tetrahedral molecule

gyorgy.hantal at fc.up.pt gyorgy.hantal at fc.up.pt
Fri Apr 29 17:55:10 CEST 2011

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.

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, 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
> 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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