[gmx-users] pull=constraint gives zero forces

Thomas Schlesier schlesi at uni-mainz.de
Tue Oct 9 11:20:10 CEST 2012

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:
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.


Am 09.10.2012 04:00, schrieb gmx-users-request at 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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