Re: Isomerization between runs

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
<http://www.ks.uiuc.edu/Research/namd/2.12/ug/node57.html#SECTION0001341110000000000000>
together
with moving restraints
<http://www.ks.uiuc.edu/Research/namd/2.12/ug/node58.html#SECTION000135410000000000000>
to
switch the isomeration state.
Best,
Ajasja

On Wed, 1 Aug 2018 at 11:57, Michail Lazaratos <
michalislaz_at_zedat.fu-berlin.de> wrote:

> Dear NAMD users,
>
> i want to introduce an isomerization of a bond in my retinal protein
> system.
>
> 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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