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 ([EMAIL PROTECTED]).
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: [EMAIL PROTECTED]
> To: gmx-users@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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---------------------------------
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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