[gmx-users] umbrella pulling, pullx vs gmx distance

[Joe Wu]

bump!

On Mon, Aug 6, 2018 at 6:10 PM, Joe Wu <joewugromacs at gmail.com> wrote:

> Hello experts,
>
> First, I want to mention that I am using Gromacs 2018.1.
>
> 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 the following 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"'
>
> The general idea is I am restraining an ion at various heights from the
> center of a water slab. I have 28 umbrella windows, each 0.05nm apart from
> distances 0 to 1.4nm. When I compare 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.
>
> I am attaching a link to the graph comparing "pullx.xvg" and
> "distance.xvg."
> https://drive.google.com/file/d/1Xc3_bChpMckxXdUqH6xkYD0IO5BW4pW3/
> view?usp=sharing
>
> 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!
>
> Best,
> Joe
>
>