Re: Question about colvars

From: Faramarz Joodaki (fjoodaki_at_my.uri.edu)
Date: Wed Jan 30 2019 - 19:29:31 CST

Dear Josh,

Thank you very much for your email! Yes, I did not define any bias or
restrains in Colvars input file.

Best Regards,
Faramarz

On Wed, Jan 30, 2019 at 8:19 PM Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> Hi Faramarz,
>
> Yes. The default in colvars is to just report the values for the colvars
> you've defined to a .traj file. Only if your definitions include a bias,
> such as adding a wall inside the colvar or a harmonic potential applied
> outside it are forces and energies computed that are fed back into NAMD.
> One way to confirm this is to check the MISC entry in the log file, since
> that is where colvars energies end up.
>
> -Josh
>
>
>
> On 2019-01-30 18:11:05-07:00 owner-namd-l_at_ks.uiuc.edu wrote:
>
> Hi everyone!
> I am running a NPT MD simulation by NAMD. I am using Colvars to monitor
> some distances and dihedral angles. Since I am just monitoring some
> variables, I have not applied any restraints on those variables. I assumed
> that by not mentioning restrains in Colvars input file and just defining
> some variables, Colvars just monitors those variables and reports them
> without applying any *default* restrains. Is it correct? I would be so
> grateful if you could help me with this issue.
> Best Regards,
> Faramarz
>
>

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