Re: [AMBER] Extract trajectories REMD

From: Daniel Roe via AMBER <>
Date: Wed, 15 Jun 2022 14:27:52 -0400


On Wed, Jun 15, 2022 at 5:41 AM Juliette Newell via AMBER
<> wrote:
> Hi Dan,
> Thank you for getting back to me.
> I have had a look at the cpptraj manual and also the replica exchange tutorial on the amber MD website and I am unsure where I am going wrong.
> The example in the manual says :
> trajin rem.001 remdtraj remdtrajtemp 300
> will this loop over all replicas? Or will I have to change the temperature at the end.

As I said in my earlier response, you specify the "lowest" replica
trajectory, and cpptraj automatically searches for the remaining
trajectories based on extension. So for example if you have 4
temperature REMD trajectories named,,, and you want to process frames at a target
temperature of 330 K, you would use:

trajin remdtraj remdtrajtemp 330

Any actions or 'trajout' commands will then only be given the frames
at 330 K. Does that make sense?


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Received on Thu Aug 04 2022 - 13:31:24 PDT
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