[gmx-users] Re: pull=constraint gives zero forces

[alex.bjorling]

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


alex.bjorling wrote
> 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?
> 
> Cheers,
> Alexander Björling,
> PhD candidate, University of Gothenburg, Sweden





--
View this message in context: http://gromacs.5086.n6.nabble.com/pull-constraint-gives-zero-forces-tp5001538p5001793.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.