From: nordgren_at_sas.upenn.edu
Date: Thu Aug 04 2005 - 17:52:49 CDT
Mauricio,
In your attached NAMD config script, you had commented-out most of your
minimization protocol; I'm guessing this was just to simplify the output
that you sent in your email, but that the problem is unchanged if you do
include those previous minimization steps, right?
It might help debug the issue if you did this again, and printed energies
every timestep. You might also save coords (to your DCD trajectory file)
every timestep, and then look to see if there is anything obviously strange.
Also, it looks like in the actual script you attached, that you aren't doing
any gentle heating of the system, but rather are just dumping in 303K of
kinetic energy all at once... which would very likenly casue trouble. Of
course, you won't see that in the output log, with just the one (initial)
set of energies being printed.
- Erik
C. Erik Nordgren, Ph.D.
Department of Chemistry
University of Pennsylvania
Quoting Mauricio Carrillo Tripp <trippm_at_gmail.com>:
> Hi,
> I'm trying to minimize-heat-equilibrate a membrane. The minimization goes
> well, and if I run after
> that with the langevinPiston turned off it seems to run fine too, but when
> I
> turn langevinPiston on
> something happens and I get an error saying that the margin is to small. I
> tried increasing its
> value and this seems to solve the problem to some extent, but then the
> simulation gets REALLY
> slow. The output below was with margin 5. I have used this same
> procedure/config (with other systems)
> before succesfully. Is this really a bug as the output says?
>
________________________________________________________________________________
> ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL
> TEMP
> TOTAL2 TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
>
> ENERGY: 0 39.3568 554.9375 11762.9435 0.0000 -759979.6963 -763.7764 0.0000
> 0.0000 0.0000 -748386.2349 0.0000 -748386.2349 -748386.2349 0.0000 -
> 57210.1063 -57210.1063 254062.7345 -57210.1063 -57210.1063
>
> TCL: Setting parameter langevinPiston to off
> TCL: Running for 10 steps
> ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL
> TEMP
> TOTAL2 TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
>
> ENERGY: 0 39.3568 554.9375 11762.9435 0.0000 -759979.6963 -763.7764 0.0000
> 0.0000 0.0000 -748386.2349 0.0000 -747670.2858 -750355.0949 0.0000 -
> 56818.4041 -56818.4041 254062.7345 -56818.4041 -56818.4041
>
> OPENING EXTENDED SYSTEM TRAJECTORY FILE
> TCL: Writing to files with basename step02-heat.
> WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 10
> WRITING COORDINATES TO OUTPUT FILE AT STEP 10
> WRITING VELOCITIES TO OUTPUT FILE AT STEP 10
> TCL: Setting parameter langevinPiston to on
> TCL: Running for 10 steps
> ERROR: Stray PME grid charges detected: 11 sending to 5 for planes 23
> ERROR: Stray PME grid charges detected: 9 sending to 5 for planes 23
> ERROR: Stray PME grid charges detected: 1 sending to 10 for planes 43
> ERROR: Stray PME grid charges detected: 8 sending to 5 for planes 23
> ERROR: Stray PME grid charges detected: 13 sending to 4 for planes 16 17
> ERROR: Stray PME grid charges detected: 15 sending to 4 for planes 16
> ERROR: Margin is too small for 22 atoms during timestep 15.
> ERROR: Incorrect nonbonded forces and energies may be calculated!
> BUG ALERT: Stray PME grid charges detected!
>
> BUG ALERT: NAMD has detected a bug. Please notify namd_at_ks.uiuc.edu.
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: BUG ALERT: Stray PME grid charges detected!
>
> BUG ALERT: NAMD has detected a bug. Please notify namd_at_ks.uiuc.edu.
>
________________________________________________________________________________
> --
>
> Mauricio Carrillo Tripp, PhD
> Department of Chemistry
> Wabash College
> trippm_at_wabash.edu
> http://trippm.bajacast.com/
>
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