[gmx-users] Weird configuration when pulling rate is small

Erik Marklund erik.marklund at chem.ox.ac.uk
Thu Feb 11 10:15:06 CET 2016

Dear Ming,

Sounds like a visualisation problem. Does it persist if you e.g. translate the system with trjconv?

Kind regards,

> On 11 Feb 2016, at 00:44, Ming Tang <m21.tang at qut.edu.au> wrote:
> Dear list,
> I am pulling a triple helix using umbrella distance. When the pulling rate is 0.0004 nm/ps, the configuration is normal. However, when I decrease the pulling rate to 0.0002 nm/ps or lower, the configuration is messy (some atoms flow away from the triple helix), but the simulations run well and both the force_strain curve and the history of number of h_bonds  look normal. Could anybody tell me why is that low pulling rates cause this problem?
> Thanks in advance,
> Ming
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