SV: Re: [gmx-users] constraint distance

[David van der Spoel]

Soren Enemark wrote:
>  Hi,
>  maybe I am misunderstanding either the manual or the topic.. but - in 
> my world -
>  I never stop being puzzled by the part of chapt 6 in the manual which 
> apparently
>  says that such distance constraining is possible even though it (seems) 
> to be
>  secretly known that it is _not_ possible unless one uses the method 
> suggested
>  below.
>  I believe, I suggest adding a comment in the manual.
> 

can you be more specific which part of the manual you mean?

>  -Soren
> 
> */Tsjerk Wassenaar <tsjerkw at gmail.com>/* skrev:
> 
>     Hi Kanin,
> 
>     The only way to get away with that is to merge your two parts to form
>     one molecule, with the only connection being a distance_restraint (or
>     another bonded term if you want to emulate bond-like behaviour such as
>     a salt-bridge).
> 
>     Best,
> 
>     Tsjerk
> 
>     On 9/11/06, kanin wichapong wrote:
>      > Dear All
>      > I would like to know how to constraint the distance between the
>      > different molecule, ex. the ligand and the protein. As far as I know
>      > whatever to do the constraint, distance, angle dihedral, it can
>     do just in
>      > the same molecule.
>      > Thank you in advance for all of your help.
>      >
>      > With Best all regard,
>      > Kanin
>      >
>      > _______________________________________________
>      > gmx-users mailing list gmx-users at gromacs.org
>      > http://www.gromacs.org/mailman/listinfo/gmx-users
>      > Please don't post (un)subscribe requests to the list. Use the
>      > www interface or send it to gmx-users-request at gromacs.org.
>      > Can't post? Read
>      > http://www.gromacs.org/mailing_lists/users.php
>      >
>      >
> 
> 
>     -- 
> 
>     Tsjerk A. Wassenaar, M.Sc.
>     Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
>     Dept. of Biophysical Chemistry
>     University of Groningen
>     Nijenborgh 4
>     9747AG Groningen, The Netherlands
>     +31 50 363 4336
>     _______________________________________________
>     gmx-users mailing list gmx-users at gromacs.org
>     http://www.gromacs.org/mailman/listinfo/gmx-users
>     Please don't post (un)subscribe requests to the list. Use the
>     www interface or send it to gmx-users-request at gromacs.org.
>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++