From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Apr 22 2009 - 09:27:37 CDT
Hi Dimitry,
you might start by looking through the namd-l archives, as similar
situations have been addressed many times in the past. See, eg., the
thread at http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/7251.html
Peter
DimitryASuplatov wrote:
> Hello,
>
> I am running simulation as follows: first em, then heating from 1K to
> 300K, then 10 ns at 300K.
>
> My configuration file is at the bottom.
>
> When heating starts I receive the following error:
>
> ------------- Processor 124 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Periodic cell has become too small for original patch grid!
> Possible solutions are to restart from a recent checkpoint,
> increase margin, or disable useFlexibleCell for liquid simulation.
>
> This must be related with the pressure coupling since it worked fine without it.
>
>
> Any suggestions? Thanks. I appreciate your time
> SDA
>
> #############################################################
> ## JOB DESCRIPTION ##
> #############################################################
>
> # STRMB in a Water Box
>
>
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
>
> structure ./strmb.s.charmm.psf
> coordinates ./strmb.s.charmm.pdb
>
> set start_temperature 1
> set hold_temperature 300
> set outputname strmb.md.charmm.namd
>
> firsttimestep 0
>
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters ./par_all27_prot_lipid.inp
> temperature $start_temperature
>
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 15.
> switching on
> switchdist 10.
>
>
> # Integrator Parameters
> timestep 2.0 ;# 2fs/step
> rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinTemp $start_temperature
> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> langevinHydrogen off ;# don't couple langevin bath to hydrogens
>
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 100.
> langevinPistonDecay 50.
> langevinPistonTemp $start_temperature
>
> # Periodic Boundary Conditions
> cellBasisVector1 108 0. 0.
> cellBasisVector2 0. 102 0.
> cellBasisVector3 0. 0 105.
> cellOrigin 63.87940979 13.3578186035 32.2524185181
>
> wrapAll on
>
>
> #PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 125
> PMEGridSizeY 115
> PMEGridSizeZ 120
>
>
> # Output
> outputName $outputname
>
> restartfreq 10000
> dcdfreq 2000
> xstFreq 2000
> outputEnergies 2000
> outputPressure 10000
>
>
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
>
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
>
> # Minimization
> minimize 5000
>
> #Heat
> for { set TEMP $start_temperature } { $TEMP < $hold_temperature } {
> incr TEMP 25 } {
> reassignTemp $TEMP
> langevinPistonTemp $TEMP
> langevinTemp $TEMP
> run 5000
> }
>
>
> reassignTemp $hold_temperature
> langevinTemp $hold_temperature
> langevinPistonTemp $hold_temperature
> run 5000000
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