Re: [AMBER] Use amber output velocity for different system

From: David A Case <>
Date: Mon, 29 Jan 2018 14:57:58 -0500

On Mon, Jan 29, 2018, Khabiri, Morteza wrote:
> I have an equilibrated DNA system. I have generated a point mutation
> in my equilibrated DNA system and want to run mutant DNA for
> sometimes. However, except for the atoms in mutated nucleotide(nt),
> I want to use the velocity from my output wildtype DNA system
> (restartfile) as an initial velocity for the rest of the atoms in my
> mutated DNA system. For the atoms in mutated nt, I am going to generate
> velocity based on maxwell-Bultmann distribution. Is there any way that
> I can extract the velocity for all atoms except perturbed one from
> wildtype system, and use it as an initial velocity for the atoms in
> mutated system?

You can get the velocities of the original system from one of it's restart
files. Then, with some hand-editing (use formatted restarts) you could put
those values into a new restart file for the mutated system.

But this seems like a lot of work for zero gain. If you are using Maxwell
Boltzmann initial velocities for some atoms, I don't immediately see any good
argument for not using randomized velocities for all atoms.


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Received on Mon Jan 29 2018 - 12:00:03 PST
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