AMBER Archive (2009)

Subject: [AMBER] ptraj fails to recognize binary REMD output

From: Kevin Wiehe (
Date: Fri Feb 06 2009 - 11:44:21 CST

I think there may be a bug in either ptraj or the REMD implementation
in Amber10. If the binary output flag is set for a REMD run
(ioutfm=1), the outputted trajectory files fail to have the
appropriate modified lines (e.g. "REMD 1 2 100 298.000") that I
believe ptraj uses to identify trajectory files as REMD trajectories
when using the remdtraj/remdtrajtemp options of trajin. ptraj does
not die when reading the binary trajectory files, but rather just
inputs the first replica trajectory instead of inputting iterations of
all replica trajectory files in the directory. Below is the shell
script that generates this problem on a REMD run with binary output
that includes a temperature at 298K.

ptraj LK_linear.prmtop << EOF
trajin remd.mdcrd.001 remdtraj remdtrajtemp 298.0
trajout LK_linear.298K.mdcrd nobox

output from ptraj:
PTRAJ: trajin remd.mdcrd.001 remdtraj remdtrajtemp 298.0
 Checking coordinates: remd.mdcrd.001
NetCDF inquiring about cell angle variable ID: NetCDF: Variable not
foundNetCDF inquiring about cell length variable ID: NetCDF: Variable
not found
PTRAJ: trajout remd.298K.mdcrd nobox

PTRAJ: Successfully read the input file.
      Coordinate processing will occur on 3000 frames.
      Summary of I/O and actions follows:

As stated above, this results in a file remd.298K.mdcrd which is not
all replicas at the temperature 298K, but instead just the first
replica trajectory, identical to the remd.mdcrd.001 trajectory file.



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