RE: Isomerization between runs

From: Vermaas, Joshua (
Date: Wed Aug 01 2018 - 06:10:27 CDT

Hi Michail,

There are two ways I can see this going. Dihedral colvar + something like a moving harmonic would get you a "smooth" transition, with the caveat that your force constant may need to be absurd to fight against the intrinsic barrier to rotating double bonds in our force fields. Arguably, isomerization isn't smooth, and so you could also go for an instantaneous change by using the "extrabonds" feature to similarly bias your system to force it to adopt the opposite isomerization. Both options are available starting from the end of your current simulation. I would not recommend manipulating the coordinates externally, since there is something to be said about actually watching the transition take place.


On 2018-08-01 04:02:54-06:00 wrote:

Dear NAMD users,

i want to introduce an isomerization of a bond in my retinal protein system--_000_BYAPR09MB2584972159B6E6866CEF4095E42D0BYAPR09MB2584namp_--

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