From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Tue Dec 22 2020 - 20:45:09 CST
Just to add to this, you can also use ssrestraints in VMD to generate a file for extraBonds in NAMD to restrain the secondary structure during SMD.
Best,
JC
On Dec 22, 2020, at 12:36 PM, Bassam Haddad <bhaddad_at_pdx.edu<mailto:bhaddad_at_pdx.edu>> wrote:
Hi Ethan,
SMD simulations add artificial forces to the system and are the likely cause of the kink. In order to not morph your helices, and get a reliable PMF, you must pull slow enough (with many replicates) to calculate the reversible work. You might be interested in running a single very slow pulling simulation to generate different configurations (i.e. windows) for which you can use Umbrella sampling to calculate your PMF. Be wary anytime you are using enhanced sampling methods to calculate PMFs, as you'll want to ensure the landscape is converged.
Good luck!
~ Bassam
On Tue, Dec 22, 2020 at 9:25 AM Ethan Croitoru <ecroitoru1_at_gmail.com<mailto:ecroitoru1_at_gmail.com>> wrote:
Hi everyone,
I am trying to run an SMD simulation separating two helices in a membrane. I am doing this for free energy calculations, so I am using colvars to sample the conformations as they separate. To pull them apart I used a harmonic on the distance colvar with a forceConstant of 5. However, in my simulations the helices become disfigured and there is a kink in the middle. I was wondering if anyone had suggestions as how to pull the helices apart without them morphing.
Thank you for the help,
Ethan Croitoru
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