[gmx-users] Rupture force definition

Justin Lemkul jalemkul at vt.edu
Tue Jan 23 12:48:06 CET 2018

On 1/23/18 3:01 AM, Rakesh Mishra wrote:
> Ok, thanks for learifivcation.
> Dear Justin I have one  another query regarding
> pulling using umbrella sampling. See these two lines below.
> Eg.    Pull group   natoms    pbc atom  distance at start    reference at
> t=0
>                       1        31       1387
>                       2        31       686                7.424 nm
> 7.424 nm
> When we use grompp for obtaining .tpr file before mdrun of pulling. We see
> 2 lines which are shown just above .
> My query is that why it is written 7.424 nm in the second line below the
> distance at start (written in the first line).
> I am asking because, in my thinking my object( reference group ) is very
> close to wall ( nearly 2 nm away from the wall of yz. here I am
> pulling in + x direction), which I can see in VMD.  Does this distance is
> distance from the pull group to the reference group or
> distance between pulled group to the wall near the reference group.

grompp is reporting the distance that it finds along the reaction 
coordinate (first value) and the expected reference value from your .mdp 
settings (second value). However you have your groups and pull settings 
defined leads grompp to tell you that this coordinate file has a 7.4-nm 
separation between your two groups.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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