RE: Question about colvars

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Jan 30 2019 - 19:19:56 CST

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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