[gmx-users] Generation of the Distance Restraints

[James Starlight]

Mark,



> 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 :-)
>

So because I'm not quite understood those equations I could not
properly define my restrains (wich are in the form presented in mu
example in previous message) in accordance to the form presented in
Gromac's manual. i think it'll be kindly from you to provide the
Gromacs restrain section
(http://www.gromacs.org/Documentation/How-tos/Distance_Restraints)
with some more detailed example of application of such disres.  It's
not quite understtod how the values 0 0.3 and 0.4 are correspond to
the real restrains wich would be obtained from experimental data (
Commonly it's single value of the some range like 0.4<R<0.5 )


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

I've found only theoretical explanation of such possibility (
gradually increasing force constant during simulation). But I
intresting in practical implementation. Could I do it in scope of
single MDrun by some options in mdm fle or should I do step-by-step
series of simulation with gradually changing forces appplied on the
disres in each MDrun?


James