Re: dummyAtom in distance colvar in ABF calculations

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Sun May 13 2018 - 10:16:35 CDT

Hi Olga, the error message:
*colvars: Error: total total forces are not available from a dummy atom
group.*
should be self-explanatory.

You should set up the "distance" component such that the total force is not
computed from the dummy group:
https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:cvc_distance

On Sat, May 12, 2018 at 5:44 PM, Olya Kravchenko <ovkrav_at_gmail.com> wrote:

> Hi all,
>
> I am using distance colvar for ABF calculations and I want to use
> dummyAtom for my group 2 atoms that coincides with the COM of the protein
> (instead of calculating COM of the whole protein every step). I am getting
> the following error:
>
> colvars: Errcolvars: Error: total total forces are not available from a
> dummy atom group.
> colvars: No such file or directory
> FATAL ERROR: Error in the collective variables module: No such file or
> directory
> or: total total forces are not available from a dummy atom group
>
> Here is my .in file:
>
> colvarsTrajFrequency 500
> colvarsRestartFrequency 5000
>
> colvar {
> name IonDistance
>
> width 0.1
>
> lowerboundary 70.0
> upperboundary 74.0
>
> lowerwallconstant 100.0
> upperwallconstant 100.0
>
> distance {
> group1 {
> atomnumbers { 66462 }
> }
> group2 {
> dummyAtom (1.485 -0.486 -0.418) }
> }
> }
>
> abf {
> colvars IonDistance
> fullSamples 500
> hideJacobian
> }
>
> Is this the right way to refer to the dummyAtom? I would appreciate your
> help!
>
> Thank you,
>
> Olga
>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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