[gmx-users] Assignment of new velocities for multi-runs

James Starlight jmsstarlight at gmail.com
Sat Sep 29 08:59:02 CEST 2012

Dear All!

I'd like to perform several simulations of the membrane protein
started from the common conditions which differs only in the initial
velocities ( for each simulation random speed distribution will be
used from the Maxwell distribution).

Because I simulate membrane protein the long equilibration phase is
required for that system. I've noticed that new velocities sets are
assigned in the NVT phase of equilibration (100ps) after which more
prolongest npt equilibration (10ns) is followed.

Does it require that new velocities always be assigned exactly during
equilibration of my system ? Could I use new velocities in the
production md run instead ? In the latter case my system will be
equilibrated with one velocities but further production MD will be
with another velocities each time? (so in latter case I can avoid long
equilibration phase for each simulation).


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