From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Wed Aug 01 2018 - 06:40:19 CDT
I think you could use the dihedral colvar
with moving restraints
switch the isomeration state.
On Wed, 1 Aug 2018 at 11:57, Michail Lazaratos <
> Dear NAMD users,
> i want to introduce an isomerization of a bond in my retinal protein
> I already have a 65 ns trajectory. Is it possible to set somehow in my
> input file the dihedral angle C1-C2-C3-C4 for example to a specific value
> and slowly equilibrate, until i can be able to restart my simulation from
> the latest checkpoint?
> Also, would there be a conflict since the latest checkpoint for the
> coordinates would have different positions for atoms manipulated?
> Thank you in advance,
> Michail Lazaratos
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