On 14/03/2012 5:50 PM, James Starlight wrote:
Mark, thanks for explanation.
So if I understood that graph correctly
You haven't. The potential is zero between r_0 and r_1. Both the
equation and graph make this clear. The potential is non-zero outside
this range. The force is the negative of the derivative of the potential
with respect to the distance. So the force is also zero between r_0 and
r_1. So if you want a distance to be restrained between 1 and 2 nm, set
r_0=1 and r_1=2. That way the force is zero if the distance is
satisfactory, and non-zero when it is not.
I leave the choice of r_2 to you as an exercise :-) Having sufficient
mathematical literacy to be able to interpret equation 4.77 correctly is
effectively a prerequisite for attempting molecular simulations.
Mark
I must define R1=1 and R2=2 values from my example 1<Rij<2 to obtain
quadratic restrain forces done in my distance range ( from 1 to 2
angstr). In other words this would restrains the i and j atom to the
desired distance by the force wich would increased by the quadratic
progresion upon distance will increased up to 2. Does it correct ?
So the value R0 ( no forces= no restraints) must correspond to the
values above and below my range. How the same range value for R0 could
be defined ?
JAmes
14 ????? 2012 ?. 3:42 ???????????? Mark Abraham
<[email protected] <mailto:[email protected]>> ???????:
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
--
gmx-users mailing list [email protected]
<mailto:[email protected]>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [email protected]
<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
