Hello,
Thank you for your response!
I used Cpptraj (v18) to extract the temperature trajectory from the REMD trajectory, and some new warning appeared:
[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 ˇ°extract_300k_traj.xˇ± 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 Thu Apr 29 2021 - 21:30:01 PDT
