Re: [AMBER] Continue running an incomplete MD with NMR restraints

From: David Case <>
Date: Sun, 15 Jan 2017 13:44:18 -0500

On Sun, Jan 15, 2017, Kat G wrote:
> I am running md in sander with nmr restraints (bond, angle, torsion and
> rdc). The force constant is set up to increase over time like &wt
> TYPE='REST', istep1=0, istep2=10000000, value1=0.3, value2=1.0, /
> Due to the expired runtime limit, the simulation stopped in the middle. I
> should have run many short runs rather than a long one. Anyway, please help
> me to continue with the remaining of this simulation.

In addition to what Bill said, you need to start from the last good restart
file you have. That will depend on how often you wrote that file, as
specified in the ntwr variable. Then compute the REST value at that point,
and start over from there.


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Received on Sun Jan 15 2017 - 11:00:03 PST
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