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.
best,
Gyorgy
Citando Sanku M <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>
To: Discussion list for GROMACS users <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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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