SV: Re: SV: Re: [gmx-users] constraint distance

[Soren Enemark]

David van der Spoel <spoel at xray.bmc.uu.se> skrev: 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?

 Basically almost anywhere in chapter 6 from 6.1 to 6.25 included.
   
 I mean, pulling works between 2 different molecules, why is it then obvious that constraining doesn't?
   
   
 
>  -Soren
> 
> */Tsjerk Wassenaar /* 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
>      >
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> 
>     -- 
> 
>     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
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-- 
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
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