ABF calculations in NAMD

From: Johny Telecaster (johnytelecaster_at_gmail.com)
Date: Mon Nov 18 2013 - 07:36:58 CST

Dear Namd users!

I have some questions about ABF calculations in NAMD.

Firstly I've simulated ligand unbinding (its motion of the ligand in Z
direction). Than I've manually chose 5 conformations along this path and
created 5 windows in accordance to the NAMD Chanel tutorial (providing new
colvars for Z for each windows as well as started conformation).

Than if I try to launch simulation in any of this window providing to the
system new set of velocities

firsttimestep 0
temprerature 310

As the result I've obtained many RATTLE errors begining simulation in
different windows. Does the system must pass equilibration for each of the
window with the application of the positions restrictions on the protein
and ligand each time (I've never seen it n the channel tutorial)?

Could I make simulations in each window using velocities from the initial
pulling sMD run ?

Many thanks for suggestions,


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