Re: SMD on Intermembrane Helices

From: Alex Balaeff (
Date: Tue Dec 22 2020 - 20:57:43 CST

My 2 cents (probably rendered unnecessary by the smart NAMD pulling
machinery): make sure that the pulling forces are uniformly distributed
over the helices. If you are applying the whole force to just a single atom
in each helix, here's your kink right there.

On Tue, Dec 22, 2020, 9:46 PM Gumbart, JC <>

> 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 <> 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 <>
> 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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