But for GMX 4.0.7 there are forces in the pullf.xvg. The forces which
arise rom the contraint the hold the two groups fixed. I use them for
thermodynamic integration...
I use the following mdp-parameters, probably this gives you an idea what
you might make different:
; AFM OPTIONS
pull = constraint
pull_geometry = distance
pull_dim = Y Y Y
pull_start = yes
pull_nstfout = 10
pull_nstxout = 500000
pull_ngroups = 1
pull_group0 = REF
pull_group1 = ZUG
pull_rate1 = 0.000
pull_init1 = 0.000
pull_constr_tol = 1e-06
But as Chris said, better post the complete mdp-file (probably for both
GMX 4.0.7 and 4.5.x) so we can comment on them.
Grettings
Thomas
Am 09.10.2012 04:00, schrieb gmx-users-requ...@gromacs.org:
Please post your entire .mdp file and a snip of the output in your pullf and
pullc files.
(Your initial post on this topic was also missing these, although the text
reads as if you intended to include them).
I'll note that there are no forces when using constraints, so the fact that you
get zero forces for a constrained run
is not really surprising. I guess the thing is that it doesn't work to keep
atoms in place for you,
which we can help you with if you post more details.
Chris.
-- original message --
Following up on this post. I've tried the same runs using version 4.0.7,
which gave immediate segmentation faults. Not sure if this is a clue or a
trivial consequence of switching versions, but there it is.
Any other ideas why the pullf output just contains zeros?
Cheers,
Alex
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