[gmx-users] pull code for Gromacs 5

[Nash, Anthony]

Hi all,

I¹m very unfamiliar with the pull code as of Gromacs 5. Unfortunately my
system is not experiencing any noticeable Œpull¹. From the options below,
which is the group experiencing the pull and which is the reference group?
 Would applying a set of position restraints on the reference group
prevent (in theory) the pulling group to move? From someone only having
ran pull code on earlier versions of gromacs, am I missing anything
blindingly obvious?


pull                    = umbrella
pull-geometry           = direction-periodic
pull-dim                = N N Y
pull-start              = yes
pull-ncoords            = 1
pull-ngroups            = 2
pull-group1-name        = fix_collagen
pull-group1-pbcatom     = 0
pull-group2-name        = pull_group
pull-coord1-groups      = 1 2
pull-coord1-rate        = 0.1
pull-coord1-k           = 1000



Context: I am pulling an explicit collagen molecule away from its
neighbour. They are in a very tight Œrectangle¹, thus they are
experiencing a pseudo fibril environment. The need for direction-periodic
is due to the length I am pulling the molecule (past half the box size).

Thanks
Anthony



Dr Anthony Nash
Department of Chemistry
University College London