yes- for all practical purposes this is a standard explicit solvent MD
run, and equilibration, dealing with pressure, etc are all the same as
you would do for any other explicitly solvated MD job. the only place
that the hybrid solvent comes into play is temporarily during the
exchange calculation- and when you're done checking exchange success,
you continue MD with the fully solvated trajectory so there is no
disruption of the solvated MD (just a change in thermostat based on a
calculation with hybrid solvent that plays NO role in the MD run).
hopefully that makes it more clear.
as an aside, I use a *much* more complicated equil procedure than 2
steps, not sure what you're doing but I would consider 2 steps to be a
possible concern.
carlos
On Fri, Jan 16, 2009 at 4:14 PM, Jason A. Ford-Green <jgreen.ccmsi.us> wrote:
>
> All,
>
> Hello. I have a more technical question this time around. Should one conduct the usual 2 stage heat up and equilibrate protocol for a fully solvated protein (TIP3 waters) when preparing for a hybrid solvent REMD simulation? This is in reference to the tutorials for REMD in GB solvent and MD simulations in explicit solvent. I have yet to see a tutorial regarding hybrid solvent prep work, and the manual does not address such issues. Any help would be greatly appreciated this late in the day. Thanks!
>
> Cheers,
>
> Jason Ford-Green
> Doctoral Student
> Interdisciplinary Nanotoxicity Center
> Jackson State University
> Contracted Technical Service Student
> U.S. Army Engineer Research and Development Center
> PI: Jerzy Leszczynski,Ph.D
> Cell: 850-443-9233
> Lab: 601-979-1797
>
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Received on Sun Jan 18 2009 - 01:22:20 PST
