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

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Feb 1 07:45:21 CET 2016

Hi Ming Tang,

Might that be due to PBC? Try

gmx trjconv -pbc nojump


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 far away), but the simulations run well and the force_strain
curve is normal. Could anybody help to tell me where is the problem?

Thanks in advance,
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