VMD-L Mailing List

From: Stefano Guglielmo (stefano.guglielmo_at_unito.it)
Date: Sun Jan 29 2017 - 17:40:53 CST

Dear vmd users,

I am trying to calculate the energy of each frames of a trajectory
generated by NAMD in a metadynamics simulation; for this purpose I have
written the following tcl script:

package require bigdcd
proc metadynamics_energy { frame } {
     global all
     if {$frame == 1} {
     cv molid 0
     cv configfile ../colvar_grid.txt
     cv load ../cdk_8bS_pocket_metadyn_75ns_replica1
}
     cv update
     set energy [cv bias metadynamics1 energy]
     puts "$frame: $energy"
 }
 set mol [mol new ../cdk2_8bS_pocket_wb_ion.psf type psf waitfor all]
 set all [atomselect $mol all]
 $all global
 bigdcd metadynamics_energy auto ../cdk_8bS_pocket_metadyn_75ns_replica1.dcd
 bigdcd_wait
 quit

When I source the script in vmd I got the following error message:

bigdcd aborting at frame 1
Error: total forces are currently not implemented.
Error loading state file
bigdcd_done
Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
Info) Exiting normally.

Does anyone have suggestions?

Thanks in advance

Stefano 

-- 
Stefano GUGLIELMO PhD
Assistant Professor of Medicinal Chemistry
Department of Drug Science and Technology
Via P. Giuria 9
10125 Turin, ITALY
ph. +39 (0)11 6707678