Re: dummyAtom-ABF

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Fri Aug 26 2011 - 10:32:20 CDT

Hi Parisa,

The oneSiteSystemForce option should solve your problem.

Cheers,
Jerome

On 26 August 2011 16:57, Parisa Akhski <Parisa.Akhshi_at_chem.queensu.ca> wrote:
>
> Dear NAMD experts,
>
> I am using "dummyAtom" to define an atom in a colvar in ABF as below:
>
>
>   distanceZ {
>       main {
>          atomnumbers { 1 }
>       }
>       ref {
>          dummyAtom (-10.16, -7.78, -8.25)
>       }
>       axis (1.0, 0.0, 0.0)
>       }
>    }
>
>
>
> Right after running the program, I get the message below in the output file:
>
> ETITLE:      TS           BOND          ANGLE          DIHED
> IMPRP               ELECT            VDW       BOUNDARY
> MISC        KINETIC               TOTAL           TEMP
> POTENTIAL         TOTAL3        TEMPAVG            PRESSURE
> GPRESSURE         VOLUME       PRESSAVG      GPRESSAVG
>
> ENERGY:       0        75.3000       291.9271       715.0756
> 2.4485         -58556.1346      8150.4504         0.0000       -24.8675
> 7335.0554         -42010.7452       305.9655    -49345.8006
> -42009.0353       305.9655           1803.6623      1827.0633
> 292378.0000      1803.6623      1827.0633
>
> OPENING EXTENDED SYSTEM TRAJECTORY FILE
> colvars:   Error: system forces are not available from a dummy atom group.
> colvars:   If this error message is unclear, try recompiling with
> -DCOLVARS_DEBUG.
> FATAL ERROR: Error in the collective variables module: exiting.
>
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Error in the collective variables module: exiting.
>
>
>
> I am wondering how and where I should define something so that ABF can find
> the forces for dummyAtom?
>
> Thanks,
>
> Parisa
>
>

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