Re: [AMBER] Questions about REMD extracting temperature trajectory

From: Charo del Genio <the.paraw.gmail.com>
Date: Sat, 24 Apr 2021 08:10:12 +0100

On 24/04/2021 02:07, Ojet wrote:
> Hello,
> I did REMD according to the tutorial. After the simulation is over, an error is reported when using “ extract_300k_traj.x” script to extract the temperature trajectory:
> remdtraj requested in trajin but this NETCDF trajectory does not contain temperatures! Trajectory will be processed as replica traj.
> The “extract_300k_traj.x” script is as follows:
> #!/bin/csh
> ptraj 5EK4_1.prmtop << EOF
> trajin remd.mdcrd.001 remdtraj remdtrajtemp 300
> trajout remd.300K.mdcrd nobox
> go
> EOF

I think it would be a good idea to try using cpptraj, rather than ptraj. Could you try that, please?


Cheers,

Charo




-- 
Dr. Charo I. del Genio
Senior Lecturer in Statistical Physics
Applied Mathematics Research Centre (AMRC)
Design Hub
Coventry University Technology Park
Coventry CV1 5FB
UK
https://charodelgenio.weebly.com
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Received on Sat Apr 24 2021 - 00:30:02 PDT
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