From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Oct 26 2012 - 12:56:33 CDT
Hello David, does the loop work with tclForces? You don't need to convert
the colvars configuration file into a script for tclForces, just any tcl
script.
The error comes from the shared code that enables colvars, tclForces, IMD,
TMD and the symmetry constraints to add forces to the simulated system.
The atomic data may not be properly reinitialized everytime you load in a
new DCD frame and run 100 MD steps from that.
On a side note, can I ask why you need a cylindrical constraint when you're
only running 100 MD steps from each DCD frames?
Giacomo
On Fri, Oct 26, 2012 at 12:13 PM, David Minh <daveminh_at_gmail.com> wrote:
> Hello NAMD users and developers,
>
> I am having a strange issue related to colvars. I am trying to do a
> coorfile loop in my NAMD configuration file:
>
> coorfile open dcd {begin1.dcd}
> while { ![coorfile read] } {
> reinitvels $temperature
> run 100
> }
> coorfile close
>
> It works fine if I remove the lines:
>
> colvars on
> colvarsConfig gorgeCylinder.colvars
>
> Here are contents of gorgeCylinder.colvars:
>
> colvar {
> name DistXY
> upperWall 6.0
> upperWallConstant 10.0
> distanceXY {
> main {
> atomsFile {../../../ligands/AAA/ligand.grid.pdb}
> atomsCol B
> atomsColValue 1.0
> }
> ref {
> dummyAtom (52.548195, 57.459400, 49.528568)
> }
> axis (-0.294390, -0.561701, 0.773192)
>
> }
> }
>
> colvar {
> name DistZ
> lowerWall 3
> upperWall 25
> lowerWallConstant 10.0
> upperWallConstant 10.0
> distanceZ {
> main {
> atomsFile {../../../ligands/AAA/ligand.grid.pdb}
> atomsCol B
> atomsColValue 1.0
> }
> ref {
> dummyAtom (52.548195, 57.459400, 49.528568)
> }
> axis (-0.294390, -0.561701, 0.773192)
>
> }
> }
>
> Basically it keeps the molecule within a cylinder.
>
> If I include the colvars lines in the NAMD configuration file, the code
> runs for 100 steps and then says:
>
> FATAL ERROR: Got the wrong number of atoms
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Got the wrong number of atoms
>
> Charm++ fatal error:
> FATAL ERROR: Got the wrong number of atoms
>
> Any ideas on what could cause this? The error doesn't really make sense
> because it works fine without the colvars lines. Is the error really
> related to colvarsInput? I can't seem to put a colvarsInput into the tcl
> loop.
>
> Thanks,
> David Minh
>
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