[gmx-users] Re: pull=constraint gives zero forces
alex.bjorling at gmail.com
Mon Oct 8 15:05:20 CEST 2012
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?
> I'm using the pull code to maintain the initial structure of a protein
> that otherwise deforms. Using pull=umbrella does what I expect it to,
> but pull=constraint produces zero forces. I'm using version 4.5.5 with
> the MARTINI force field.
> The pull=umbrella mdp contains the following,
> and gives the following pullf output:
> For such runs, the group COM:s stay within 0.1 nm of their initial
> positions, throughout a long trajectory.
> The pull=constraint mdp starts with
> and produces the pullf output
> For these runs, the group COM:s move around freely. I guess I'm doing
> something wrong but can't work out what. I've tried specifying k:s for
> the contraint runs, and tried removing all other constraints in the
> molecule. I've tried to comply with the manual's instructions but to
> no avail.
> Any ideas?
> Alexander Björling,
> PhD candidate, University of Gothenburg, Sweden
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