Re: Calculating the force needed to constrain a protein

From: Maxim Belkin (
Date: Fri Jul 18 2014 - 11:43:27 CDT

You can use NAMD's SMD feature to restrain center of mass of your selection (protein). SMD will output applied force in pN. To get unbiased PMF along some trajectory, you would need to use something like weighted histogram analysis method (WHAM).


On Jul 18, 2014, at 11:18 AM, Shane.OMahony <> wrote:

> Hi all,
> I was wondering if it's possible to calculate the force needed to keep a protein a fixed distance from a surface using NAMD? I want to constrain the center of mass of the protein and then calculate the PMF using an unbiased potential.
> Thanks,
> Shane

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