[gmx-users] pull COM code pullx.xvg vs gmx distance

Joe Wu joewugromacs at gmail.com
Wed Jul 25 08:54:09 CEST 2018


I was wondering what the differences between pullx.xvg and gmx distance are.

"pullx.xvg" is the output of an umbrella sample mdrun.
"distance.xvg" is the output of this command (I am comparing the
z-component distance):

gmx distance -s umbrella01.tpr -f umbrella01.trr -oxyz dist.xvg -select
'com of group "Water" plus com of group "Ion"'

I did a pull of an ion on the +z axis through water solvent. Then, I did an
umbrella sample on 28 umbrella windows, each 0.05nm apart from distances 0
to 1.4nm. I am comparing the "pullx.xvg" and "distance.xvg" output of any
one of these windows, and it seems that for the most part, both z-distances
are the same (with a deviation of +/-0.001 due to sig-figs); however there
are a few time steps where the pullx distance deviates a lot from the
distance.xvg distance.

The pull portion of my MDP file is:

; Pull code

pull                    = yes

pull_ngroups            = 2

pull_ncoords            = 1

pull_group1_name        = Water

pull_group2_name        = Ion

pull_coord1_type        = umbrella

pull_coord1_geometry    = direction

pull_coord1_vec         = 0 0 1

pull_coord1_groups      = 1 2

pull_coord1_dim         = N N Y

pull_coord1_rate        = 0.0

pull_coord1_k           = 4000

pull_coord1_start       = no

pull_coord1_init        = 0.1

Does anyone know why these two z-component distances are not identical, as
they should? I am graphing both "pullx.xvg" and "distance.xvg" z-distance
as a function of time; both graphs should be superimposable, but they are
not. Why is this the case?

Please let me know if you need more information.

Thank you for your time!


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