[gmx-users] Imposing distance restraints between two residues

[Justin A. Lemkul]

Maybe you would be more interested in a distance *restraint*?  Note that 
constraints and restraints mean different things in Gromacs.  The relevant 
manual section is 4.3, with a specific example of how to use distance restraints 
on p. 61.

-Justin

plmallip at mail.uh.edu wrote:
> Dear colleagues,
> 
>             I want to impose simple distance constraint between the two 
> ends of the same protein with missing residues in between. As I went 
> through the manual I found I can use "constraints type 2" fixes the 
> distance without connecting atoms by a chemical bond.
> 
> Manual shows this example for O-H and H-H distances
> 
> [ settles ]
> 
> ; OW funct doh dhh
> 
> 1 1 0.1 0.16333
> 
> [ exclusions ]
> 
> 1 2 3
> 
> 2 1 3
> 
> 3 1 2
> 
>   How can I do this for e.g. between two CA of the residues. Also, do 
> you suggest SHAKE or LINCS for this purpose? If you can give an example 
> for residues, just like the one above for water, that would be great. 
> Thanks in advance for any kind of suggestion in this regard.
> 
> 
> warm regards,
> Prema,
> Graduate student,
> UOH.
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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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