On 2011-04-29 19.15, gyorgy.han...@fc.up.pt wrote:
Citando David van der Spoel <sp...@xray.bmc.uu.se>:
On 2011-04-29 17.55, 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.
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 <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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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
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