[gmx-users] Generation of the Distance Restraints

James Starlight jmsstarlight at gmail.com
Wed Mar 28 13:48:43 CEST 2012


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.

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?

Thank for help again,


22 марта 2012 г. 17:32 пользователь Mark Abraham
<Mark.Abraham at anu.edu.au>написал:

> 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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