Why not do two umbrella sampling simulations: one with initial conformations
from your faster pulling and one with initial conformations from your slower
pulling. Then you can run them both as regular US simulations until (a) neither
US PMF is drifting systematically with increasing simulation t
Thanks Erik!
/PK
2012/11/16 Erik Marklund
> Hi,
>
> Blindly defining the center of mass for a group of atoms is not possible
> in a periodic system such as a typical simulation box. You need some clue
> as to which periodic copy of every atom that is to be chosen. By providing
> pull_pbcatom0 y
Hi,
Blindly defining the center of mass for a group of atoms is not possible in a
periodic system such as a typical simulation box. You need some clue as to
which periodic copy of every atom that is to be chosen. By providing
pull_pbcatom0 you tell gromacs to, for every atom in grp0, use the pe
Hi Chris
Seems my confusion was that I assumed that the distances in the
profile.xvg-file should correspond to something I could measure with
g_dist. Turns out it does not.
Thank you for helping me sorting out this, I got it now :-)
About pull_pbcatom0 though. My box is >> 2*1.08 nm in all direct
Hi Erik,
Thank you for your answer.
I see your point now. Went and had a look in gmx_wham.c to see how things
are calculated, and that makes sense.
I was looking for an easy way of relating different parts of the resulting
PMF to my original starting frames, as a means to understand exactly what
Hi,
See below.
14 nov 2012 kl. 15.06 skrev Gmx QA:
> Hi Chris,
>
> and thank you for your reply. I should have included my g_dist command in
> my first mail. Here goes:
>
> I first run trjconv to extract the individual frames from my pulling
> trajectory
> $ trjconv -f pull.xtc -s pull.tpr -o
What you reported is not what you did. It appears that grompp, gtraj, and
g_dist report the same value.
Please also report the value that you get from your pullx.xvg file that you get
from mdrun, which I suspect
will also be the same.
The difference that you report is actually between the first
Hi Chris,
and thank you for your reply. I should have included my g_dist command in
my first mail. Here goes:
I first run trjconv to extract the individual frames from my pulling
trajectory
$ trjconv -f pull.xtc -s pull.tpr -o conf.gro -sep -pbc mol -ur compact
Then, g_dist like so:
$ g_dist -s
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