Thanks Chris and Justin
I do get the output I want from grompp(below). The distance of 5.507 nm
is the distance that I want to start with and I assume it is therefore
the equilibrium distance for the harmonic potential. The COM distances
from the simulations fluctuate around this value which is what I want,
although my histogram is the wrong shape.
Pull group natoms pbc atom distance at start reference at t=0
0 84 42
1 84 126
5.507 5.507
Cheers
Gavin
[email protected] wrote:
> I missed that pull_start = yes, sorry. So Gavin, your run should have
> stayed around the starting position. Make the histogram directly and
> you should get a better idea.
>
> Chris.
>
> -- original message --
>
>
> To clarify, the tutorial sets "pull_init1 = 0" because it is used in
> conjunction
> with "pull_start = yes," in order to take the starting COM distance as
> the
> reference. Check the grompp output to verify that you're getting what
> you think
> you should be. Otherwise, you'd have to set "pull_start = no" and
> modify your
> .mdp file to reflect the proper value of pull_init1 for every window.
>
> -Justin
>
>
>
>
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