[gmx-users] Generation of the Distance Restraints

[Justin A. Lemkul]

James Starlight wrote:
> Mark, Justin,
> 
> Thanks for advises. Indeed I think that simple text editor would be 
> better sollution in my casw because of small number of restraints.
> 
> I just have a question about definition of the Distances
> 
> This is the default of the restraints between atom 10 and 16.
> 
> [ distance_restraints ]
> ; ai aj type index type’ low up1 up2 fac
>   10 16 1    0     1     0.0 0.3 0.4 1.0
> 
> 
> 
> I'd like to restrict distance between both of that atoms   7.96 < 
> r(Ca-Ca)< 8.41
> 
> I've found that the up1 is the 7.96 and up2 is the 8.41 but how I could 
> specify 'low' in the above table ? Should I obtain value for the initial 
> Ca-Ca distance between my residues from the initial structure? How I 
> could do it?
> 

See Figure 4.13 and equations 4.79 in the manual.  r0 = low, r1 = up1, and r2 = up2.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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