[gmx-users] Pulling a periodic molecule (for the third time)

Alex nedomacho at gmail.com
Tue May 19 00:02:44 CEST 2015

Hi all,

This is sort of my attempt to definitively conclude that what I want to do
is not possible with the pull code.

For simplicity, here's what I have: a box containing a fully periodic
near-linear ssdna chain along Z. I want to enable non-stop translocation in
that direction, at a constant rate.

The only way I was able to make this type of translocation work is with the
constant-force option. However, due to the peculiarities of the system,
constant force pulling (physically, in my opinion) makes the motion
somewhat jerky, as opposed to constant rate. At this point, I have tried
every possible option I could find in the manual (related to the problem),
and I just can't make it work. The most I get is a pretty energetic and
fun-looking oscillation of the chain along Z.

Do you think constant force is my only option? If someone wants to try it
out, I can [privately] provide a tarball with the input.

Any thoughts?



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