From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Fri Aug 05 2005 - 11:17:30 CDT
You can only change certain parameters after calling run. In
http://www.ks.uiuc.edu/Research/namd/current/ug/node11.html see this:
Between ``run'' commands the reassignTemp, rescaleTemp, and langevinTemp
parameters can be changed to allow simulated annealing protocols within a
single config file. The useGroupPressure, useFlexibleCell,
useConstantArea, useConstantRatio, LangevinPiston, LangevinPistonTarget,
LangevinPistonPeriod, LangevinPistonDecay, LangevinPistonTemp,
SurfaceTensionTarget, BerendsenPressure, BerendsenPressureTarget,
BerendsenPressureCompressibility, and BerendsenPressureRelaxationTime
parameters may be changed to allow pressure equilibration. The fixedAtoms
and constraintScaling parameters may be changed to preserve macromolecular
conformation during minimization and equilibration (fixedAtoms may only be
disabled, and requires that fixedAtomsForces is enabled to do this).
...
The ``coorfile'' command allows NAMD to perform force and energy analysis
on trajectory files. ``coorfile open dcd filename'' opens the specified
DCD file for reading. ``coorfile read'' reads the next frame in the opened
DCD file, replacing NAMD's atom coordinates with the coordinates in the
frame, and returns 0 if successful or -1 if end-of-file was reached.
``coorfile skip'' skips past one frame in the DCD file; this is
significantly faster than reading coordinates and throwing them away.
``coorfile close'' closes the file. The ``coorfile'' command is not
available on the Cray T3E.
-Jim
On Thu, 4 Aug 2005, vivek sharma wrote:
> Dear NAMD users,
>
> I am running this script in NAMD,but it runs just for one step (i.e. i=3),
> but then fails for i=4 with the error mentioned below:
> ----------script-------------
> for {set i 3} {$i <= 4} {incr i} {
> temperature 310
>
> timestep 1.0
>
>
> structure biselliprotsku.psf
> paraTypeCharmm on
> parameters par_all27_prot_lipid.inp
> exclude scaled1-4
> 1-4scaling 1.0
> switching on
> switchdist 47.0
> cutoff 50.0
> pairlistdist 60.5
>
> stepspercycle 1
>
>
> pairInteraction on
> pairInteractionFile pairs.pdb
> pairInteractionCol B
> pairInteractionGroup1 1
> pairInteractionGroup2 2
>
> outputEnergies 1
>
>
> coordinates orient$i.pdb
>
> outputname results$i
> binaryoutput no
> run 0
> }
>
>
> ----------error-------------
> TCL: Setting parameter temperature to 310
> FATAL ERROR: Setting parameter temperature from script failed!
> -------------
>
> Could you please suggest the solution?
>
> THanks in advance.
>
> Regards,
>
>
> Vivek
>
>
>
> --
> VIVEK SHARMA
> HBG BI
> "Basic research is what I'm doing when I don't know what I'm doing."
> - Werner von Braun
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:39:48 CST