[gmx-users] Generation of the Distance Restraints

[Mark Abraham]

On 14/03/2012 12:38 AM, James Starlight wrote:
> Justin,
>
> 1) I've already tried to examine this graphs but have not understood 
> the meaning of the Ro value.

How about reading the equation on the previous page?

>
> E.g I have known distance restrains for the pair of residue wich are 
> 1<r< 2  for instance. As I understood the R1=1 and R2=2 but what about 
> R0 ?As I've understood  this value might be slightly less than R1 ( 
> e.g 0.9). Does this correct and how I could specify R0 more accuracy?

Anything else you've known and understood about distance restraints in 
some unknown context doesn't matter. What's written in the GROMACS 
manual matters for using them in GROMACS :-)

>
>
> 2) Besides I want to know if there are possible way to gradyally 
> decrease force constants during MD run? E.g I want to dicrease this 
> value each 100ps on the desired value. Is there any way to defind this 
> step value in the MDP file or should I re-run mu simulation X times 
> started from the previous short run with bigger forses applied?

I already answered this. 
http://lists.gromacs.org/pipermail/gmx-users/2012-March/069301.html

Mark

>
>
> James
>
> 13 ????? 2012 ?. 17:19 ???????????? Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> ???????:
>
>
>
>     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
>
>     -- 
>     ========================================
>
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
>     -- 
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