AW: Low global CUDA exclusion count! (9592 vs 9618)

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Mar 13 2018 - 05:56:25 CDT

Increase pairlist to 16

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von ANIRBAN MANDAL
Gesendet: Dienstag, 13. März 2018 10:40
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: Low global CUDA exclusion count! (9592 vs 9618)

 

​​

We have Setup NAMD with GPU support.

 

namd2 +p8 +idlepoll step4_equilibration_NVT.inp > step4_equilibration_NVT.out
namd2 +p8 +idlepoll step5_production.in <http://step5_production.in> > step5_production.out

Step4_Equilibration_NVT is working fine without any error on GPU but Step5_production_NPT is not running and coming up with an error from the very beginning as follows:

 

"Warning: Low global CUDA exclusion count! (9592 vs 9618)
Warning: This warning is not unusual during minimization.
Warning: Increasing pairlistdist or cutoff may avoid this."

 

After short minimization, it stops with the beginning of the production run part with error:

 

"TCL: Running for 500000 steps
ERROR: Constraint failure in RATTLE algorithm for atom 57!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely; see error messages above."

 

I have tried with fixation of atoms and also tried margin value up to value 2 but in vain.

Below I am attaching the input file that I have used. In case you find some error or correction in the script please kindly let me know. On CPU there is no error for production part but on GPU for the same system, I am getting the aforementioned error.

 

Thanking you in anticipation,

 

Regards,

Anirban Mandal

 

#######################################################
# PDB, PSF, PAR, VEL & INPUT PARAMETERS
#######################################################
coordinates Graphene_thy_wat.pdb # PDB file
structure Graphene_thy_wat.psf #PSF file in XPLOR format
                # (can be generated using CHARMM - write psf xplor card @unit)
set inputname step4_equilibration;
binCoordinates $inputname.coor; # coordinates from last run (binary)
binVelocities $inputname.vel; # velocities from last run (binary)
extendedSystem $inputname.xsc; # cell dimensions from last run (binary)

parameters toppar/par_all36m_prot.prm
parameters toppar/par_all36_na.prm
parameters toppar/par_all36_carb.prm
parameters toppar/par_all36_lipid.prm
parameters toppar/par_all36_cgenff.prm
parameters toppar/toppar_water_ions.str
parameters toppar/toppar_dum_noble_gases.str
parameters toppar/toppar_all36_prot_d_aminoacids.str
parameters toppar/toppar_all36_prot_fluoro_alkanes.str
parameters toppar/toppar_all36_prot_heme.str
parameters toppar/toppar_all36_prot_na_combined.str
parameters toppar/toppar_all36_prot_retinol.str
parameters toppar/toppar_all36_na_nad_ppi.str
parameters toppar/toppar_all36_na_rna_modified.str
parameters toppar/toppar_all36_lipid_bacterial.str
parameters toppar/toppar_all36_lipid_cardiolipin.str
parameters toppar/toppar_all36_lipid_cholesterol.str
parameters toppar/toppar_all36_lipid_inositol.str
parameters toppar/toppar_all36_lipid_lps.str
parameters toppar/toppar_all36_lipid_miscellaneous.str
parameters toppar/toppar_all36_lipid_model.str
parameters toppar/toppar_all36_lipid_prot.str
parameters toppar/toppar_all36_lipid_sphingo.str
parameters toppar/toppar_all36_lipid_yeast.str
parameters toppar/toppar_all36_lipid_hmmm.str
parameters toppar/toppar_all36_lipid_detergent.str
parameters toppar/toppar_all36_carb_glycolipid.str
parameters toppar/toppar_all36_carb_glycopeptide.str
parameters toppar/toppar_all36_carb_imlab.str

                # (CMAP is supported from NAMD version 2.6)
paraTypeCharmm on
mergeCrossterms yes #To include CMAP correction

seed 12345
timestep 2.0 #timestep_2_fs
stepspercycle 20 #number_of_steps_before_making_new_pairlist

######################################################
# OUTPUT PARAMETERS
######################################################
outputEnergies 100; #display every 0.25ps
outputTiming 500; #display every 1ps
xstFreq 500; #save every 10ps
dcdFreq 1000; #save every 10ps
restartfreq 500; #update restart file every 10ps
dcdUnitCell yes; # the file will contain unit cell info
wrapAll on;
wrapWater on;

rigidBonds all #SHAKE_H-bonds
rigidTolerance 0.000001

fullElectFrequency 1
nonbondedFreq 1

#Fixing Atoms
fixedAtoms on
fixedAtomsFile Graphene_thy_wat_fixed.pdb ;# flags are in this file
fixedAtomsCol B ;# set beta non-zero to fix an atom

######################################################
#Temperature & Pressure Control
######################################################
Langevin on
LangevinDamping 5
LangevinTemp 298
LangevinHydrogen off
LangevinPiston on
LangevinPistonTarget 1.01325 #target pressure in (bar)
LangevinPistonPeriod 100 #oscilation period in (fs)
LangevinPistonDecay 50 #dumping time scale (fs)
LangevinPistonTemp 298 # barostat noise T = target T

######################################################
# NONBOND CUTOFF
######################################################
switching on
cutoff 12.0 #This_is_for_VDW
switchdist 10.0
pairlistdist 14.0 #need at least 1.5 between cutoff and pairlist
#margin 1 #default=0, once equilibrated margin can be reduced

exclude scaled1-4
1-4scaling 1.0
#switching on
vdwForceSwitching yes; # New option for force-based switching of vdW
                                       # if both switching and vdwForceSwitching are on CHARMM force
                                       # switching is used for vdW forces.

######################################################
# CELL PARAMETERS
######################################################

useGroupPressure yes; # use a hydrogen-group based pseudo-molecular viral to calcualte pressure and
                                       # has less fluctuation, is needed for rigid bonds (rigidBonds/SHAKE)
useFlexibleCell no; # yes for an anisotropic system like membrane
useConstantRatio no; # keeps the ratio of the unit cell in the x-y plane constant A=B

######################################################
# PMEwald
######################################################
PME yes
PMETolerance 0.000001
PMEInterpOrder 6
PMEGridSizeX 54
PMEGridSizeY 40
PMEGridSizeZ 64

######################################################
# OUTPUT FILES
######################################################

binaryoutput off
outputname namd_template_prod_1
restartname namd_template_prod_rst_1
binaryrestart off

#Run for 1.0 ns
#minimize 100000
minimize 200000
run 500000

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