[gmx-users] restraints or constraints over two molecules

[Eric Jakobsson]

Please note a new method for simulating large-scale conformational 
changes that take place over longer-than- molecular dynamics time 
scales at 
http://www.biophysj.org/cgi/rapidpdf/biophysj.107.118778v1.pdf  The 
difference between this and other steering methods is that it is 
designed to follow more closely the microscopically reversible 
ensemble of paths that pertain when conformational changes take place 
at constant temperature.

It is implemented in Gromacs and we are happy to share the code patch 
with users (and/or with the Gromacs developers for inserting in the 
next version of Gromacs)--only ask for a citation in 
return.  Requests should go to Jay Mashl (mashl at uiuc.edu).

Eric

At 07:04 AM 4/2/2008, you wrote:
>Hi,
>
>We still need an elegant solution for this problem.
>Currently the only option is to merge the two moleculetype 
>definitions into one.
>Or if you are also happy with an harmonic restraint, you can use the 
>pull code.
>
>Berk.
>
>
>----------
> > Date: Wed, 2 Apr 2008 15:53:19 +0200
> > From: schlesi at uni-mainz.de
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] restraints or constraints over two molecules
> >
> > hi,
> > i want to ask if there is a possibility to make distance restraints or
> > contraints over two molecules?
> > till now i have two .itp files (one for each molecule) and i include
> > them with 'inculde "...itp" . after that i have [ system ] and [
> > molecules ] (with my two molecules) and then [ distance_restraints ]
> > respectively [ contraints ].
> >
> > but in both cases i get after grompp:
> > [ file "info.top", line 14 ]:
> > Atom index (6) in distance_restraints out of bounds (1-5).
> >
> > so i think the problem is that i have two molecules.
> > but is there probably another way to get this work?!?
> >
> > thanks for an answer.
> > thomas schlesier
> > _______________________________________________
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>
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---------------------------------
Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of 
Biochemistry, and of the Center for Biophysics and Computational Biology
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
3261 Beckman Institute, mc251
University of Illinois, Urbana, IL 61801
ph. 217-244-2896  Fax 217 244 9757

"When a distinguished but elderly scientist states that something is 
possible, he is almost certainly right. When he states that something 
is impossible, he is very probably wrong." ---Arthur C. Clarke

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