[gmx-users] pull code

Attilio vargiu at sissa.it
Thu Jun 23 18:35:39 CEST 2005

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

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.


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

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