[gmx-users] Re: pull distance

[Thomas Schlesier]

> 
> Dear Gromacs Users
> 
> I have set my pull option as "constant force" and  the pull geometry is
> "distance"
> the manual has stated that the pull_k1 unit is kJ/mol/nm . does it mean that
> the force applied to the
> protein is proportional to the distance between the 2 groups ? else what is
> it ?

No, kJ/mol is an energy unit, so kJ/mol/nm is a force unit -> the force 
does not depend on the distant, but is constant. One important think is 
that, if you want your force in pN you must transform this value to 
kJ/mol/nm.

> 
> my second question is that what is the preferable choice for the pull ref
> group (pull_group0) in a protein when the force is exerted to the first and
> last res of the molecule .

You want the first / last residue as pull_group0 / pull_group1 (or in 
diferent order). If you then take the full residue or only one or a 
couple of atoms is up to you.

Greetings
Thomas

> 
> Best Regards
> Ali