VMD-L Mailing List

From: Stefano Guglielmo (stefano.guglielmo_at_unito.it)
Date: Mon Jan 30 2017 - 16:05:23 CST

For completeness I attach the complete output generated by vmd after
sourcing the script.

Best regards

2017-01-30 0:40 GMT+01:00 Stefano Guglielmo <stefano.guglielmo_at_unito.it>:

> 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
>
> 

-- 
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