From: Bassam Haddad (bhaddad_at_pdx.edu)
Date: Tue Dec 22 2020 - 11:31:23 CST
Hi Seke,
You put a variable in your code `if { $boxtype == "hexa" } ` but you aren't
defining it anywhere. I am surprised it ran given that I cannot see where
you defined $a, $b, or $c. It shows however that $d is defined as zero, so
I am pretty sure you are not using hexagonal periodic boundaries but simply
orthorhombic. I would restart your simulation using a corrected
configuration file.
I'd just replace:
if { $boxtype == "hexa" }
with:
if {1}
or just add `set boxtype "hexa"` at the top of the file.
~ Bassam
On Sun, Dec 20, 2020 at 6:38 PM Seke Keretsu <sekekeretsu_at_gmail.com> wrote:
> Dear expert,
>
> I ran into this problem during my simulation but couldn't find a solution
> on the mailing list. If already resolved in another discussion please
> advise or direct me to the resource.
>
> FATAL ERROR: can't read "boxtype": no such variable while executing
> "if { $boxtype == "hexa" } {
> set b [expr {$a / 2 * sqrt(3)}]
> set d [expr {$a / 2}]
> set wrapnearst on
>
> The simulation continued to run after the error message. Kindly advise on
> how to proceed. System was set up using charmm-gui server. My
> configuration file is given below.
>
> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
> *configuration.namd*
> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
> structure step5_charmm2namd.psf
> coordinates step5_charmm2namd.pdb
>
> set temp 303.15;
> set outputname step6.1_equilibration;
>
> # read system values written by CHARMM (need to convert uppercases to
> lowercases)
> exec tr "\[:upper:\]" "\[:lower:\]" < ../step5_assembly.str | sed -e "s/
> =//g" > step5_charmm2namd.str
> source step5_charmm2namd.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 50000; # 1000 steps = every 2ps
> dcdfreq 10000;
> 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 10000; # XSTFreq: control how often
> the extended systen configuration
> # will be appended to the XST
> file
> outputEnergies 10000; # 125 steps = every 0.25ps
> # The number of timesteps
> between each energy output of NAMD
> outputTiming 10000; # 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 defi
>
>
> timestep 1.0; # 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;
>
> # Periodic Boundary conditions. Need this since for a start...
> if { $boxtype == "hexa" } {
> set b [expr {$a / 2 * sqrt(3)}]
> set d [expr {$a / 2}]
> set wrapnearst on
> } else {
> set wrapnearst off
> set d 0.0
> }
>
> cellBasisVector1 $a 0.0 0.0; # vector to the next image
> cellBasisVector2 $d $b 0.0;
> cellBasisVector3 0.0 0.0 $c;
> cellOrigin 0.0 0.0 $zcen; # the *center* of the cell
>
> wrapWater on; # wrap water to central cell
> wrapAll on; # wrap other molecules too
> wrapNearest $wrapnearst; # 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 yes; # yes for anisotropic system
> like membrane
> useConstantRatio yes; # keeps the ratio of the unit
> cell in the x-y plane constant A=B
>
> langevin on
> langevinDamping 1.0
> langevinTemp $temp
> langevinHydrogen off
>
> constraints on
> consexp 2
> consref restraints/prot_posres.ref
> conskfile restraints/prot_posres.ref
> ............................
> ............................
> ............................
>
> Thank you.
>
> Faithfully,
> Seke
>
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