From: adrian palacios (adpala_at_hotmail.com)
Date: Thu Jul 18 2013 - 20:12:05 CDT
Yeah, but I tried to center my molecule's pdb before all preparations, so the actual system origin should be the same as the coordinates origin (0 0 0), but I will do it anyways, IŽll let you know what happens tomorrow.
Thanks for your help!
Adrian Palacios
Date: Thu, 18 Jul 2013 21:05:53 -0400
Subject: Re: namd-l: Minimization/Equilibrium problem, atoms moving too fast
From: broomsday_at_gmail.com
To: adpala_at_hotmail.com
CC: namd-l_at_ks.uiuc.edu
I'm not super familiar with exactly how NAMD does the periodic stuff or again what that VWD Boundary term means, but I wonder what would happen in your original larger simulation if you replaced:
"cellOrigin 0 0 0"
with
"cellOrigin 80.5 73.0 72.0"
Maybe nothing, but worth testing since it's a quick change.
On Thu, Jul 18, 2013 at 8:58 PM, adrian palacios <adpala_at_hotmail.com> wrote:
Before you answered I looked for the vdw "NAMD Plot" from the minimization log file and it does represent the greater contribution to this unstability, but how could I fix this? I tried running a similar system in a smaller box and it worked, but still is the second time I have this problem related to CaCl Ionization neutralizing the system.
Thanks for your reply, it was very accurate.
Adrian Palacios
Date: Thu, 18 Jul 2013 17:12:32 -0400
Subject: Re: namd-l: Minimization/Equilibrium problem, atoms moving too fast
To: adpala_at_hotmail.com
CC: namd-l_at_ks.uiuc.edu
>From the log, your energies actually go crazy low after minimization, not crazy high. And this seems to result from the ' VDW BOUNDARY' term. I'm not sure what this term applies to, but how confident are you in the cell dimensions you gave the system?
On Thu, Jul 18, 2013 at 4:28 PM, Adrian <adpala_at_hotmail.com> wrote:
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo -- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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