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

Ming Tang m21.tang at qut.edu.au
Thu Feb 11 01:44:57 CET 2016

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,

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