RE: Mismatch in atom number between psf and dcd files

From: Wintrode, Patrick (
Date: Mon Oct 01 2018 - 14:11:24 CDT

Thanks for your reply. When I load the psf, the atom number is 18,086. If load the corresponding pdb file to look at it it's also 18086. When I try to load the dcd file it says that there are 41,015 atoms.

Patrick Wintrode

From: Vermaas, Joshua <>
Sent: Friday, September 28, 2018 12:23 PM
To: Wintrode, Patrick <>;
Subject: RE: Mismatch in atom number between psf and dcd files

Hi Patrick,

I get this most often if I do something dumb and regenerate my psf after having run a simulation. The number of water molecules after resolvation might be different by one or two, and then the number of atoms between the psf and the dcd doesn't match. NAMD's dcd always have the same number of atoms as the input psf and pdb, and also checks that the number of atoms matches in the inputs. How different are the atom counts? VMD reports that when it errors on a file load, and I'm willing to bet that its a multiple of 3.


On 2018-09-28 09:12:02-06:00<> wrote:
I generated namd structure and input files using the CHARMM GUI. When I ran the equilibration, everything appeared to run normally. However, when I attempt to load the resulting dcd output in vmd, I get the following error:

Invalid number of atoms in coordinate file
Mismatch between existing molecule or structure file atom count and coordinate or trajectory atom count

I loaded the same psf file that was used in running the simulation, and the error results when I attempt to load the output dcd. Shouldn't the simulation have crashed if there was a mismatch in atom number between the psf and the trajectory? I tried regenerating the inpu files from the CHARMM GUI, and also tried using a different pdb of a structurally related protein but get the same error. I've used the CHARMM GUI in the past to set up namd simulations without any problems. Can someone suggest where I should start looking for the source of this error? The inp file used to run the simulation is below.


Patrick L. Wintrode

structure ../step3_pbcsetup.xplor.ext.psf
coordinates ../step3_pbcsetup_rotated.pdb
extendedSystem ../step3_pbcsetup_rotated.xsc

set temp 303.15;
set outputname step4_equilibration;

# read system values written by CHARMM (need to convert uppercases to lowercases)
exec tr "\[:upper:\]" "\[:lower:\]" < ../step3_pbcsetup.str | sed -e "s/ =//g" > step3_pbcsetup.namd.str
source step3_pbcsetup.namd.str

temperature $temp;

outputName $outputname; # base name for output from this run
                                       # NAMD writes two files at the end, final coord and vel
                                       # in the format of first-dyn.coor and first-dyn.vel
firsttimestep 0; # last step of previous run

restartfreq 500; # 500 steps = every 1ps
dcdfreq 1000;
dcdUnitCell yes; # the file will contain unit cell info in the style of
                                       # charmm dcd files. if yes, the dcd files will contain
                                       # unit cell information in the style of charmm DCD files.
xstFreq 1000; # XSTFreq: control how often the extended systen configuration
                                       # will be appended to the XST file
outputEnergies 125; # 125 steps = every 0.25ps
                                       # The number of timesteps between each energy output of NAMD
outputTiming 1000; # The number of timesteps between each timing output shows
                                       # time per step and time to completion

# Force-Field Parameters
paraTypeCharmm on; # We're using charmm type parameter file(s)
                                       # multiple definitions may be used but only one file per definition
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_pyrophosphate.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_lipid_ether.str
parameters toppar/toppar_all36_carb_glycolipid.str
parameters toppar/toppar_all36_carb_glycopeptide.str
parameters toppar/toppar_all36_carb_imlab.str
parameters toppar/toppar_all36_label_spin.str
parameters toppar/toppar_all36_label_fluorophore.str

# These are specified by CHARMM
exclude scaled1-4 # non-bonded exclusion policy to use "none,1-2,1-3,1-4,or scaled1-4"
                                       # 1-2: all atoms pairs that are bonded are going to be ignored
                                       # 1-3: 3 consecutively bonded are excluded
                                       # scaled1-4: include all the 1-3, and modified 1-4 interactions
                                       # electrostatic scaled by 1-4scaling factor 1.0
                                       # vdW special 1-4 parameters in charmm parameter file.
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.

# You have some freedom choosing the cutoff
cutoff 12.0; # may use smaller, maybe 10., with PME
switchdist 10.0; # cutoff - 2.
                                       # switchdist - where you start to switch
                                       # cutoff - where you stop accounting for nonbond interactions.
                                       # correspondence in charmm:
                                       # (cutnb,ctofnb,ctonnb = pairlistdist,cutoff,switchdist)
pairlistdist 16.0; # stores the all the pairs with in the distance it should be larger
                                       # than cutoff( + 2.)
stepspercycle 20; # 20 redo pairlists every ten steps
pairlistsPerCycle 2; # 2 is the default
                                       # cycle represents the number of steps between atom reassignments
                                       # this means every 20/2=10 steps the pairlist will be updated

# Integrator Parameters
timestep 2.0; # fs/step
rigidBonds all; # Bound constraint all bonds involving H are fixed in length
nonbondedFreq 1; # nonbonded forces every step
fullElectFrequency 1; # PME every step

# Constant Temperature Control ONLY DURING EQUILB
reassignFreq 500; # reassignFreq: use this to reassign velocity every 500 steps
reassignTemp $temp;

wrapWater on; # wrap water to central cell
wrapAll on; # wrap other molecules too
wrapNearest on; # use for non-rectangular cells (wrap to the nearest image)

# PME (for full-system periodic electrostatics)
PME yes;
PMEInterpOrder 6; # interpolation order (spline order 6 in charmm)
PMEGridSpacing 1.0; # maximum PME grid space / used to calculate grid size

# Pressure and volume control
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 anisotropic system like membrane
useConstantRatio no; # keeps the ratio of the unit cell in the x-y plane constant A=B

langevin on
langevinDamping 1.0
langevinTemp $temp
langevinHydrogen off

# constant pressure
langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 50.0
langevinPistonDecay 25.0
langevinPistonTemp $temp

# planar restraint
colvars on
exec sed -e "s/\$bb/1.0/g" -e "s/\$sc/0.1/g" mdsetup_restraint.namd.col > restraints/$outputname.col
colvarsConfig restraints/$outputname.col

minimize 10000
numsteps 90000000
run 25000

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