Hi,
On Fri, Apr 30, 2021 at 12:03 AM Ojet <ojet0501.163.com> wrote:
>
> Hello,
> Thank you for your response!
> I used Cpptraj (v18) to extract the temperature trajectory from the REMD trajectory, and some new warning appeared:
These warnings are just letting you know that the NetCDF trajectory
file from REMD doesn't have a 'temperature' dimension, as was the case
in the past. This is the reason you couldn't use ptraj to process
these trajectories. If you didn't receive any error messages things
seem to have worked fine. Let me know if not.
-Dan
> [trajin remd.mdcrd.001 remdtraj remdtrajtemp 300.0]
>
> Found 8 replicas.
>
> Reading 'remd.mdcrd.001' as Amber NetCDF
>
> Warning: New style (Amber >= V18) remd values detected with < 2 dimensions.
>
> Warning: Assuming temperature.
>
> Warning: New style (Amber >= V18) remd values detected with < 2 dimensions.
>
> Warning: Assuming temperature.
>
> Warning: New style (Amber >= V18) remd values detected with < 2 dimensions.
>
> Warning: Assuming temperature.
>
> Warning: New style (Amber >= V18) remd values detected with < 2 dimensions.
>
> Warning: Assuming temperature.
>
> Warning: New style (Amber >= V18) remd values detected with < 2 dimensions.
>
> Warning: Assuming temperature.
>
> Warning: New style (Amber >= V18) remd values detected with < 2 dimensions.
>
> Warning: Assuming temperature.
>
> Warning: New style (Amber >= V18) remd values detected with < 2 dimensions.
>
> Warning: Assuming temperature.
>
> Warning: New style (Amber >= V18) remd values detected with < 2 dimensions.
>
> Warning: Assuming temperature.
>
>
>
> The “extract_300k_traj.x” script is as follows:
>
> #!/bin/csh
>
> cpptraj ala10.prmtop << EOF
>
> trajin remd.mdcrd.001 remdtraj remdtrajtemp 300.0
>
> trajout remd.300K.mdcrd nobox
>
> distance d1 out dist.300K.dat :2.CA :8.CA
>
> go
>
> EOF
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Received on Fri Apr 30 2021 - 09:00:03 PDT
