Re: SMD on Intermembrane Helices

From: Bassam Haddad (
Date: Tue Dec 22 2020 - 11:36:36 CST

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 <> 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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