From: Sourav Ray (souravrayiitkgp_at_gmail.com)
Date: Mon Apr 04 2016 - 05:26:56 CDT
Hello
1. I think the timestep is too small (0.1 fs, usually 1 fs is minimum that
is employed). Please confirm from previous literature.
2. Use a higher langevin damping constant for the thermostat, like say
10/ps, it solves a lot of issues during equilibration/relaxation.
3. If constant pressure is not working, either increase the margin from
default 0 to say 5 or turn the flexible cell and constant area option on.
You may need to turn both on initially, later remove the margin but keep
flexible cell option on during production run.
4. I would suggest not to use unit cell dimensions larger than system size,
it leads to density fluctuations at the corners of the cuboid.
5. TIme step x Number of steps = Total time, the output frequencies don't
make sense to me.
6. Try rigidbond - hydrogen (or all) and check if there is any change.
Regards
Sourav
On Sun, Apr 3, 2016 at 11:19 PM, faride badalkhani <
farideh.khamseh_at_gmail.com> wrote:
> Dear NAMD experts,
>
> I am going to run a minimization and NVT simulation followed by a NPT on a
> system consists of a hyperbranched polymer in water. But, I got this error:
> atoms moving too fast simulation has become unstable NAMD
> therefore, based on NAMD mailing list I increase the cellbasisvectorX, Y,
> and Z size and decreased the time step to 0.1 but this time I got this
> error:
>
> ERROR: Stray PME grid charges detected: 2 sending to 9 for planes 32 33 34
> 35
> ERROR: Margin is too small for 1 atoms during timestep 201933.
> ERROR: Incorrect nonbonded forces and energies may be calculated!
> FATAL ERROR: Low global CUDA exclusion count! (27955 vs 27959) System
> unstable or pairlistdist or cutoff too small.
>
> FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
> [0] Stack Traceback:
> [0:0] CmiAbort+0x41 [0xefde44]
> [0:1] _Z8NAMD_bugPKc+0x9e [0x64a77e]
> [0:2] _ZN10Controller16compareChecksumsEii+0x86f [0x94db2f]
> [0:3] _ZN10Controller9integrateEi+0xc8d [0x952e4d]
> [0:4] _ZN10Controller9algorithmEv+0x1b2b [0x944f6b]
> [0:5] CthStartThread+0x20 [0xef9e90]
> [0:6] [0x33af8438f0]
> [0] Stack Traceback:
> [0:0] LrtsAbort+0x70 [0xefe524]
> [0:1] CmiAbortHelper+0x102 [0xefddfd]
> [0:2] CmiAbort+0x41 [0xefde44]
> [0:3] _Z8NAMD_bugPKc+0x9e [0x64a77e]
> [0:4] _ZN10Controller16compareChecksumsEii+0x86f [0x94db2f]
> [0:5] _ZN10Controller9integrateEi+0xc8d [0x952e4d]
> [0:6] _ZN10Controller9algorithmEv+0x1b2b [0x944f6b]
> [0:7] CthStartThread+0x20 [0xef9e90]
> [0:8] [0x33af8438f0]
> I do not know what should I do now! Any help will be appreciated.
>
> My configuratyion file is as follows:
>
> # Input
> paraTypeCharmm on
> parameters G5-OH/par_all36_prot.prm
> parameters G5-OH/par_all36_polyester.prm
> temperature $temperature
>
>
> # Force-Field Parameters
> exclude scaled1-4 ;# These are specified by CHARMM
> 1-4scaling 1.0 ;# These are specified by CHARMM
> cutoff 12.0 ;# may use smaller, maybe 10.0, with PME
> switching on
> switchdist 10.0 ;# cutoff - 2.0
> pairlistdist 14.0 ;# Promise that atom won’t move more than
> 2A in a cycle, cutoff + 2
>
>
> # Integrator Parameters
> timestep 0.1 ;# 0.1fs/step
> rigidBonds water
> nonbondedFreq 1 ;# nonbonded forces every step
> fullElectFrequency 2 ;# PME only every other step
> stepspercycle 10 ;# redo pairlists every ten steps
>
>
> # Constant Temperature Control
> langevin on ;# langevin dynamics
> langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
> langevinTemp $temperature
> langevinHydrogen off ;# don't couple langevin bath to hydrogens
>
>
> # Periodic Boundary Conditions
> cellBasisVector1 42.00 0.00 0.00 ;# vector to the next image
> cellBasisVector2 0.00 62.00 0.00
> cellBasisVector3 0.00 0.00 40.00
> cellOrigin -12.08 -1.14 -15.83 ;# the *center* of the cell
>
> wrapWater on ;# wrap water to central cell
> wrapAll on ;# wrap other molecules too
> wrapNearest off ;# use for non-rectangular cells
>
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSpacing 1.0
>
>
> # Constant Pressure Control (variable volume)
> useGroupPressure yes ;# needed for rigidBonds
> useFlexibleCell no ;# no for water box, yes for membrane
> useConstantArea no ;# no for water box, maybe for membrane
>
>
> # Output
> outputName $outputname
>
> restartfreq 500 ;# 500steps = every 1ps
> dcdfreq 250
> xstFreq 250
> outputEnergies 100
> outputPressure 100
> outputTiming 1000 ;# shows time per step and time to completion
>
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
>
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> # Minimization
> minimize 200000
> reinitvels $temperature
>
> run 3000000 ;# 0.3 ns
>
> Truly yours,
> Farideh
>
>
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