This looks great thanks, had meant to try and implement something like
these restraints for ages but never got round to it, you know how it is ...
Tom
--On 13 March 2009 21:06 +0100 Tsjerk Wassenaar <[email protected]> wrote:
Or, you use our server (http://haddock.chem.uu.nl/Squeeze/) to get an
optimally packed system and simulate it with the Gromacs 3.3.1 version
you can download from
http://nmr.chem.uu.nl/~tsjerk/GMX/gromacs-3.3.1-rtc.tgz
That version of gromacs has the roto-translational constraints
implemented that were developed by Andrea Amadei.
Mind that the server is fresh :) The paper is about to be submitted.
Unfortunately I haven't had time to dig into the GMX 4 code to
implement the rotational constraints yet. I wouldn't want to
compromise the performance :S
Cheers,
Tsjerk
On Fri, Mar 13, 2009 at 8:26 PM, TJ Piggot <[email protected]> wrote:
You might want to try a rombic dodecahedron box (an option in editconf).
Or you can run the simulation using a triclinic box hoping the images
don't interact and then check after the simulation has finished using
g_mindist -pi on the trajectory, bearing in mind if they do then you
will have wasted a lot of time.
If you do want to use a triclinic box having a larger amount of water
surrounding the complex may be advisable as this makes images interacting
less likely
Tom
--On Friday, March 13, 2009 20:10:05 +0100 Tsjerk Wassenaar
<[email protected]> wrote:
Hi,
You have to make sure that you're molecule doesn't rotate. Otherwise
it will cause direct interactions over the PBC. The same holds true
for large conformational changes.
Cheers,
Tsjerk
On Fri, Mar 13, 2009 at 7:26 PM, Justin A. Lemkul <[email protected]>
wrote:
Lucio Montero wrote:
I want to simulate a protein complex using a triclinic box, because it
reduce my system size in 60%, and consequently the computing time. I
have read that using a triclinic box can give problems for a long MD
if the peptide has a whirl, but I don´t know if it is a problem for a
complex of ~ 530 aa (protein 1: 376 aa, protein 2: 132 aa, protein 3:
20 aa, complex size 64x64x104 Angstroms) surrounded by 12 Ângstroms of
water. I want to run the MD simulating 20 ns.
What problems have you read about? Can you cite a source so we know
what you're talking about?
-Justin
Best regards,
Lucio Montero
--------------------------------------------------------------------
-- ---------------------------------------------------------- Lucio
Ricardo Montero Valenzuela
Laboratorio del Dr. Federico Sánchez
Ext. 27666
Departamento de Biología Molecular de Plantas
Instituto de Biotecnología, UNAM
Cuernavaca, Morelos, 62210
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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----------------------
TJ Piggot
[email protected]
University of Bristol, UK.
_______________________________________________
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
_______________________________________________
gmx-users mailing list [email protected]
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----------------------
TJ Piggot
[email protected]
University of Bristol, UK.
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