[gmx-users] Shear flow with deform option

Makoto Yoneya makoto-yoneya at aist.go.jp
Wed Sep 6 05:13:08 CEST 2017

Dear GROMACS users:

The GROMACS manual says that the off-diagonal elements (of deform option) can be used to shear a solid or a liquid.
Then, how should I set the "comm-mode" option (concern for removing center of mass translation) to get shear flow with this deform option?
I'd tried "comm-mode=None" (no restriction of the center of mass motion) but it looks no difference with "comm-mode=Linear" concern on shear flow.
Also, I'm wondering how the system temperature (from atomic velocities) was evaluated if I succeeded to get shear flow with this deform option (mean shear flow contribution will be extracted or not).
Sorry if it was FAQ.


Makoto Yoneya, Dr.
AIST, Tsukuba

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