I am planning to run GaMD simulation in amber, and I want to produce multiple trajectories of the same system to run independent simulations of the system with different initial velocities. The question is at which step should I assign inital velocities and how to do that (which flags to use?) and how this will affect the subsequent input files should I change them as well?
my planned workflow is tleap - minimization - heating - equilibration - short cMD run - GaMD runs
so at which step to start assigning velocities and how this affect the following inputs
Thanks in advance
If you have good computational speed, then assign random velocity from heating step, otherwise you can skip heating and equilibration, and assign random velocity at cMD. Regarding keyword for seed velocity, you can see discussion here:
Re: [AMBER] A query about using random seed generator in simulations from David A Case on 2016-03-15 (Amber Archive Mar 2016) (ambermd.org)
Amber keywords are tricky and sometimes have no sense.
The different velocity assignment helps to generate an ensemble that will capture the true conformational space of the protein.
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