search

Colvars / colvars

Collective variables library for molecular simulation and analysis programs
http://colvars.github.io/
GNU Lesser General Public License v3.0
196 stars 56 forks source link

Calculating biasing forces from Well-tempered Metadynamics simulations #679

Closed Praveen-Prabhakar closed 3 months ago

Praveen-Prabhakar commented 3 months ago

Hi all,

I have run a well-tempered metadynamics simulations on NAMD with colvars for biasing the CV. I am writing to ask if there is any COLVARS module/method which can calculate the biasing force applied from the .dcd, or .hills.traj file? I didn't save forces during the simulation run though!

Thanks in advance.

fabsugar commented 3 months ago

Hi, there is a way to do that using the FCAM tool ( https://github.com/FCAM-NIH/FCAM). You need the .colvars.traj and the .hills.traj files. If you don't have the .colvars.traj file you can calculate it from the .dcd using the colvars dashboard. Please check the FCAM manual for doing that (there are also examples in the tutorial folders which are also explained in the manual). Hope it helps, Fabrizio

On Tue, Mar 26, 2024 at 9:03 PM Praveen-Prabhakar @.***> wrote:

Hi all,

I have run a well-tempered metadynamics simulations on NAMD with colvars for biasing the CV. I am writing to ask if there is any COLVARS module/method which can calculate the biasing force applied from the .dcd, or .hills.traj file? I didn't save forces during the simulation run though!

Thanks in advance.

— Reply to this email directly, view it on GitHub https://github.com/Colvars/colvars/issues/679, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACZ54AEHJS2XWT3F3QNSPDTY2ILFNAVCNFSM6AAAAABFJ6K27SVHI2DSMVQWIX3LMV43ASLTON2WKOZSGIYDSNRRGM3TANA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

Praveen-Prabhakar commented 3 months ago

Hi Fabrizio!

Thank you for sharing this! Yes I will got through the tutorial.