[gmx-users] pull code

Attilio vargiu at sissa.it
Fri Jun 24 19:14:32 CEST 2005

Hi all,
first I would like to thank all of you for your replies.

Anton Feenstra wrote:

> 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?

...in fact, as noted also by Jens, I (stupid) misunderstood the manual, 
I thinked that both the groups had to be "single" molecules and not 
pieces of molecules. Instead I understand from you that I can have 
**pieces** of **different molecules* *as pulling and reference group.  
In any case, this should have only effects on the time step (?).

>> 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?
I tested various velocities, now I'm using 0.003 nm/ps, and a force 
constant of 3000 kJ/mol-1/nm-2. Unfortunately I don't have any 
experimental data to compare with.

Attilio Vittorio Vargiu
PhD Student at SISSA/ISAS
via Beirut 4
I-34014 Trieste, Italy
tel +390403787335   fax +390403787528

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