[gmx-users] Pull direction is always outward

cescoxonta francesco.zonta79 at gmail.com
Wed May 2 21:24:33 CEST 2012

I am trying to pull a subdomain of protein towards the center of the channel
it makes. To do this I need to pull some aminoacids in -1, 0, 0 direction. I
tried with this pull code

; Pull code
pull            = umbrella
pull_geometry   = direction_periodic
pull_start      = yes
pull_nstfout    = 1
pull_ngroups    = 1
pull_group1     = nth
pull_vec1       = -1.0 0.0 0.0
pull_rate1      = 0.001
pull_k1         = 2000

Without giving the reference pull_group0
I get a warning on the absolute system of reference, but I ignored it,
because the same code worked when I tried to pull an ion in a fixed
However my group nth is pulled to the right and not to the left, as I was
thinking it would do.

I made two other trials, resumed here, because I am not sure of how exactly
are the input used:


pull_vec1       = 1.0 0.0 0.0
pull_rate1      = 0.001


pull_vec1       = 1.0 0.0 0.0
pull_rate1      = -0.001

But also those pulled my fragment towards right instead of left, that is
outward of the channel.

Then I tried to chose another part of the protein, that is on the opposite
side, wondering if for some reason only positive pull are allowed, but now,
the fragment is pulled to the left and not to the right, again outward.

What can be the problem? Should I use a differente pull code (distance for
example?). Is there anyway to make the pulling work using

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