[gmx-users] Pull code

[David L. Bostick]

>
> 1) In case I manage to use 'starting structure' anyway: What kind of
> constraint is applied on the pulled group? Is it determined by the AFM
> 'forceconstant' parameter?
>

 From my understanding, the starting structure code is only for generating
starting structures for free energy calculation.  Thus, there is no
restraint constant.  The position of the pulled group is updated every
timestep by bringing the pulled group closer to the reference group an
amount defined by the variable translation_rate.  The system's structure
is written out to a gro file every transstep.  In my experience it works
quite well.  An example of one of my ppa files is:

verbose                  = no
runtype                  = start
group_1                  = pull_group
reference_group          = my_ref
reftype                  = com
reflag                   = 1
direction                = 0.0 0.0 1.0
r0_group1                = 0.0 0.0 0.0
reverse                  = to_reference
tolerance                = 0.000001
translation_rate         = 0.0002
transstep                = 0.1

You can then use various restraints and constraints already present in the
package for generating statistics on these structures.  You can sample the
configurations along your reaction coordinate in ways which, many times,
can be better than the option of AFM pulling.

David