[gmx-users] Rupture force definition
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
> 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.
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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