[gmx-users] Generation of the Distance Restraints

[Mark Abraham]

On 14/03/2012 5:45 AM, James Starlight wrote:
> 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 )

If you can't understand the equation, plot the function by hand for 
those values 0, 0.3 and 0.4. Then you will see that this shape is not 
really what you want, and know what to do to make it closer to what you 
do want.

I can't think of a clearer way to explain the functional form of the 
distance restraint than the given equation with an example graph of it 
nearby. You have some distance range that you want to see happen based 
on some external information. You need to choose the distance constants 
for that functional form to reproduce that in a way that you judge will 
work, given your initial distance. The linear regime above r_2 is useful 
for not having forces that are massively large (from a quadratic 
potential) far from the region of zero potential. Whether this is 
important depends on your starting configuration.

>
>
>> 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?

Only step by step. Something like simulated annealing is only available 
for temperature variation.

Mark
>
>
> James