On 28/03/2012 10:48 PM, James Starlight wrote:
Mark,
This sounds like I use very small forces but expect reasonable effect.
But I've applied different forces with step-by-step increasing of
force constants ( from very softest comparable with the thermal motion
( 0.1 kj mol nm-2) to relatively hight (10). As the consequence I've
observed effect of application of that harmonic constraints wich I've
defined in the r0 and r1 range but in some case ( where forses were
were hight I've seen perturbation of my structures) and when
constraints were low ( in accordance to my literature) I've not seen
desired effect like the selection of the constraints was wrong ( but
actually all restraints were applied on the correct possitions). This
was seen by measurement of the distances between atom pairs wich were
contrained. Eg If I define this distances in the 0.1<Rij<0.4 ( r0=0,1
r1=0,4 for this instance) range the real distance between i and j
atoms in the simulated structure was lower or higher of the defined
range.
What's reasonable depends on the objective. If you want to keep
something very close to where it *already* is, and it's reasonably happy
there already, then you don't generally need much in the way of
restraints. If your starting configurations are different from what you
wish to achieve, then you're going to have to metaphorically speak loud
enough to be heard over the thermal commotion, and then loud enough to
cross the relevant barriers. That can mean big restraint forces and tiny
integration steps and lots of tweaking and praying. Or finding a new
starting configuration that's more relevant for the objective.
For comparison, pdb2gmx generations position restraints with 1000 kJ mol
nm-2 force constants for helping people not perturb their structures
during equilibration. Your distance deviations are much larger than will
usually occur with PR, so you don't want to go that large.
By the way I've found that besides such harmonic restraining also I
can apply more rigid holo restraints from specified value. Could you
tell me where I could find information of the application of such
restraints in the topology of my protein? As I understood this could
be done by means of editing of the bond enty in topology but what
exactly specified type should I applied on the restried atoms?
Rigid constraints are not useful for you, because your initital
conditions are a long way from your target conditions. Any kind of
harmonic potential has the same or worse issues than you already have.
Mark
Thank for help again,
James
22 ????? 2012 ?. 17:32 ???????????? Mark Abraham
<mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>> ???????:
If there's a car at the bottom of one valley in the Alps, and you
think it should be two valleys over, and you pull it with a
trained cat... it's not going to move much. How big an animal you
need depends on the geography. There need not even be a reasonable
route for you to take, if the target valley is effectively on Mars.
Mark
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