multiple trajectories

From: Bala subramanian (
Date: Fri Feb 26 2010 - 10:50:38 CST


I apologize in advance if this question is not appropriate for this forum. I
have done a simulation of 20ns on a 409 residues protein with NAMD.
Monitoring of the rmsd shows that the simulation is stable within 20ns.

I wish to do multiple simulation on the protein. Kindly suggest me the best
approach to do it based on your experience. Should i do simulation from the
scratch doing all minimization, heating, equilibration etc. or pickup
conformations from my 20ns simulation and then start fresh production phase
by reassigning velocities.

Thanks in advance,

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