VMD-L Mailing List

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Jan 30 2017 - 07:13:49 CST

Hi Stefano,

your colvars input enables options that require total atomic forces (like
an ABF bias, or outputTotalForce in a colvar). Those are not implemented in
VMD. You should be able to disable those options, as they are not necessary
for your current purpose.

Best,
Jerome

On 30 January 2017 at 00:40, Stefano Guglielmo <stefano.guglielmo_at_unito.it>
wrote:

> 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
>
>