Hi,
On Wed, Jun 15, 2022 at 5:41 AM Juliette Newell via AMBER
<amber.ambermd.org> 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 rem.nc.001, rem.nc.002,
rem.nc.003, rem.nc.004 and you want to process frames at a target
temperature of 330 K, you would use:
trajin rem.nc.001 remdtraj remdtrajtemp 330
Any actions or 'trajout' commands will then only be given the frames
at 330 K. Does that make sense?
-Dan
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Received on Thu Aug 04 2022 - 13:31:24 PDT
