[gmx-users] pull code

[Anton Feenstra]

Attilio wrote:

> Hi all,
> 
> I have a questio concerning the feasibility of a steering dynamics on my
> system. I want to push a small molecule along the minor groove of the
> DNA, so:
> 
> 1) I removed all the constraints on bonds (no LINCS or SHAKE)

Why?

> 2) I selected as a reference group a piece of DNA, and as a pulling
> group the small molecule.

Sounds right.

> Maybe I miss something of the warnings in the manual, but I didn't
> understand if the profiles I get are reliable or not (I calculate works
> of ~15 Kcal/mol, but the inverse process -i.e. the movement of the
> molecule in the opposite of the pulling direction- happens spontaneously
> after 10ns!), since I take a part of a molecule as reference group, but
> also I removed all the constraints.

Maybe you're pulling too fast (or too hard)? Do you have experimental 
numbers on the affinity of these molecules for each other? And, perhaps, 
the 'on' and 'off' rates for binding?


-- 
Groetjes,

Anton

* NOTE: New Phone & Fax numbers (below) *

  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 59 87608 - Fax: +31 20 59 87610           |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
|_____________|_______________________________________________________|