NAMD Chingolin Tutorial Question

[siddiqi...@gmail.com]

I have been trying to go through the WESTPA NAMD tutorial with Chingolin, and have a question regarding an error I am having. I was able to get the NaCl NAMD tutorial to work, but not Chingolin. Has anyone else been able to use WESTPA with NAMD for a protein? 

https://chong.chem.pitt.edu/wewiki/Advanced_Tutorial:_NAMD#Introduction

When I tried running init.sh, I was given the error:

w_init: error: unrecognized arguments: --wm-work-manager=threads

Regarding the following line in init.sh:

$WEST_ROOT/bin/w_init $BSTATE_ARGS $TSTATE_ARGS --segs-per-state 4 --wm-work-manager=threads "$@"

I thought this may have to do with different WESTPA versions, so I changed this line to:

$WEST_ROOT/bin/w_init $BSTATE_ARGS $TSTATE_ARGS --segs-per-state 4 --work-manager=threads "$@"

This, however, gives me a new error when I run ./init.sh that I don't know how to resolve:

$./init.sh

simulation chig_namd_new root is /Users/haziq/Documents/westpa/westpa/chig_namd_new

Creating HDF5 file '/Users/haziq/Documents/westpa/westpa/chig_namd_new/west.h5'

1 target state(s) present

Calculating progress coordinate values for basis states.

-- WARNING  [py.warnings] -- //anaconda/lib/python2.7/site-packages/numpy/lib/npyio.py:891: UserWarning: loadtxt: Empty input file: "/var/folders/fd/z56fbw1917l8ly588lvfbt8m0000gz/T/tmpLPSPsw"

  warnings.warn('loadtxt: Empty input file: "%s"' % fname)

Traceback (most recent call last):

  File "/Users/haziq/Documents/westpa/westpa/lib/cmds/w_init.py", line 125, in <module>

    suppress_we=args.shotgun)

  File "/Users/haziq/Documents/westpa/westpa/src/west/sim_manager.py", line 249, in initialize_simulation

    self.get_bstate_pcoords(basis_states)        

  File "/Users/haziq/Documents/westpa/westpa/src/west/sim_manager.py", line 201, in get_bstate_pcoords

    basis_states[fmap[future]].pcoord = future.get_result().pcoord

  File "/Users/haziq/Documents/westpa/westpa/lib/wwmgr/work_managers/threads.py", line 36, in run

    result = self.fn(*self.args, **self.kwargs)

  File "/Users/haziq/Documents/westpa/westpa/src/west/wm_ops.py", line 26, in get_pcoord

    propagator.get_pcoord(state)

  File "/Users/haziq/Documents/westpa/westpa/src/west/propagators/executable.py", line 395, in get_pcoord

    loader('pcoord', rfname, state, single_point = True)

  File "/Users/haziq/Documents/westpa/westpa/src/west/propagators/executable.py", line 59, in pcoord_loader

    expected_shape))

ValueError: progress coordinate data has incorrect shape (0,) [expected (1,)] 

How can I resolve this problem?

Thanks!

[Joshua Adelman]

Hi Haziq,

I can imagine a couple of things might be going on:

1. If you look in `get_pcoord.sh`, you can see that the path to vmd is hardcoded. If you’re copy of vmd does not reside at that location, you’re going to get a failure. This is the problem when I try to run the tutorial (after making the changes you mentioned to the work manager flag). You can see the error in the file named `rmsd.temp`. Basically you’re script fails so no pcoords are getting written.

2. Assuming you resolve #1, the next problem is that VMD does not come compiled with Python support by default in the binary distributed by the Schulten group, which I’m guessing is the executable you’re likely using. Re-compiling VMD from scratch with python support is not much fun. 

Given the issue mentioned in #2, I might suggest, as an exercise, re-writing the get_pcoord.sh and the python scripts that it calls to drop the VMD dependency and use a easily installed python library like MDTraj (http://mdtraj.org/) or MDAnalysis (http://www.mdanalysis.org/). You should be able to write something equivalent in less than a dozen lines of code.

Hope that helps.

Josh

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[Haziq Siddiqi]

Hi Josh,

Thanks! I used MDAnalysis to re-write a progress coordinates calculator was successfully able to execute ./init.sh. 

I updated runseg.sh with the new pcoord calculator.

I am now having issues with ./run.sh. The pcoord is being marked as having the incorrect shape, even though there is no such issue when running ./init.sh with the same pcoord calculator.

I have included below the new pcoord program (rmsd_haziq.py), the error in west.log, the output from init.sh, the get_pcoord.sh script, and the runseg.sh script.

How can I resolve this issue with run.sh in order to get the simulation to run?

$ more rmsd_haziq.py 

import MDAnalysis

from MDAnalysis.analysis.rms import rmsd

ref = MDAnalysis.Universe('chig.psf','reference.pdb')

seg = MDAnalysis.Universe('chig.psf','seg_initial.pdb')

ref_backbone = ref.select_atoms('backbone')

A = ref_backbone.positions.copy()

seg_backbone = seg.select_atoms('backbone')

B = seg_backbone.positions.copy()

output = rmsd(A,B, center=True)

print output

$ more west.log

Maximum wallclock time: 125 days, 0:00:00

Fri Jul 15 15:38:02 2016

Iteration 1 (300 requested)

Beginning iteration 1

4 segments remain in iteration 1 (4 total)

1 of 59 (1.694915%) active bins are populated

per-bin minimum non-zero probability:       1

per-bin maximum probability:                1

per-bin probability dynamic range (kT):     0

per-segment minimum non-zero probability:   0.25

per-segment maximum non-zero probability:   0.25

per-segment probability dynamic range (kT): 0

norm = 1, error in norm = 0 (0*epsilon)

-- WARNING  [py.warnings] -- //anaconda/lib/python2.7/site-packages/numpy/lib/npyio.py:893: UserWarning: loadtxt: Empty input file: "/var/folders/fd/z56fbw1917l8ly588lvfbt8m0000gz/T/tmpC7kekm"

  warnings.warn('loadtxt: Empty input file: "%s"' % fname)

-- WARNING  [py.warnings] -- //anaconda/lib/python2.7/site-packages/numpy/lib/npyio.py:893: UserWarning: loadtxt: Empty input file: "/var/folders/fd/z56fbw1917l8ly588lvfbt8m0000gz/T/tmpxL01CF"

  warnings.warn('loadtxt: Empty input file: "%s"' % fname)

-- WARNING  [py.warnings] -- //anaconda/lib/python2.7/site-packages/numpy/lib/npyio.py:893: UserWarning: loadtxt: Empty input file: "/var/folders/fd/z56fbw1917l8ly588lvfbt8m0000gz/T/tmpEIb43q"

  warnings.warn('loadtxt: Empty input file: "%s"' % fname)

-- WARNING  [py.warnings] -- //anaconda/lib/python2.7/site-packages/numpy/lib/npyio.py:893: UserWarning: loadtxt: Empty input file: "/var/folders/fd/z56fbw1917l8ly588lvfbt8m0000gz/T/tmpEoC1Mz"

  warnings.warn('loadtxt: Empty input file: "%s"' % fname)

-- ERROR    [west.propagators.executable] -- could not read pcoord from '/var/folders/fd/z56fbw1917l8ly588lvfbt8m0000gz/T/tmpC7kekm': ValueError('progress coordinate data has incorrect shape (0, 1) [expected (2, 1)]',)

-- ERROR    [west.propagators.executable] -- could not read pcoord from '/var/folders/fd/z56fbw1917l8ly588lvfbt8m0000gz/T/tmpxL01CF': ValueError('progress coordinate data has incorrect shape (0, 1) [expected (2, 1)]',)

-- ERROR    [west.propagators.executable] -- could not read pcoord from '/var/folders/fd/z56fbw1917l8ly588lvfbt8m0000gz/T/tmpEIb43q': ValueError('progress coordinate data has incorrect shape (0, 1) [expected (2, 1)]',)

-- ERROR    [west.propagators.executable] -- could not read pcoord from '/var/folders/fd/z56fbw1917l8ly588lvfbt8m0000gz/T/tmpEoC1Mz': ValueError('progress coordinate data has incorrect shape (0, 1) [expected (2, 1)]',)

-- ERROR    [west.sim_manager] -- propagation failed for 4 segment(s):

0  

1  

2  

3

exception caught; shutting down

-- ERROR    [w_run] -- Traceback (most recent call last):

  File "/Users/haziq/Documents/westpa/westpa/lib/cmds/w_run.py", line 65, in <module>

    sim_manager.run()

  File "/Users/haziq/Documents/westpa/westpa/src/west/sim_manager.py", line 645, in run

    self.check_propagation()

  File "/Users/haziq/Documents/westpa/westpa/src/west/sim_manager.py", line 544, in check_propagation

    raise PropagationError('propagation failed for {:d} segments'.format(len(failed_segments)))

PropagationError: propagation failed for 4 segments

$ ./init.sh

simulation chig_namd_new root is /Users/haziq/Documents/westpa/westpa/chig_namd_new

Creating HDF5 file '/Users/haziq/Documents/westpa/westpa/chig_namd_new/west.h5'

1 target state(s) present

Calculating progress coordinate values for basis states.

1 basis state(s) present

Preparing initial states

-- WARNING  [py.warnings] -- //anaconda/lib/python2.7/site-packages/h5py/_hl/dataset.py:76: DeprecationWarning: numpy boolean negative, the `-` operator, is deprecated, use the `~` operator or the logical_not function instead.

  if isinstance(chunks, tuple) and (-numpy.array([ i>=j for i,j in zip(tmp_shape,chunks) if i is not None])).any():

        Total bins:            60

        Initial replicas:      4 in 1 bins, total weight = 1

        Total target replicas: 240

        

Simulation prepared.

1 of 60 (1.666667%) active bins are populated

per-bin minimum non-zero probability:       1

per-bin maximum probability:                1

per-bin probability dynamic range (kT):     0

per-segment minimum non-zero probability:   0.25

per-segment maximum non-zero probability:   0.25

per-segment probability dynamic range (kT): 0

norm = 1, error in norm = 0 (0*epsilon)

mgrabe3-2:chig_namd_new haziq$ 

$ ./run.sh

simulation chig_namd_new root is /Users/haziq/Documents/westpa/westpa/chig_namd_new

 

$ more get_pcoord.sh (modification in red)

#!/bin/bash

if [ -n "$SEG_DEBUG" ] ; then

    set -x

    env | sort

fi

cd $WEST_SIM_ROOT

# Get progress coordinate

python rmsd_haziq.py > $WEST_PCOORD_RETURN

if [ -n "$SEG_DEBUG" ] ; then

    head -v $WEST_PCOORD_RETURN

fi

$ more runseg.sh (modifications in red)

#!/bin/bash

if [ -n "$SEG_DEBUG" ] ; then

    set -x

    env | sort

fi

cd $WEST_SIM_ROOT

mkdir -pv $WEST_CURRENT_SEG_DATA_REF || exit 1

cd $WEST_CURRENT_SEG_DATA_REF || exit 1

# Set up the run

ln -sv $WEST_SIM_ROOT/auxfiles/* .

 case $WEST_CURRENT_SEG_INITPOINT_TYPE in

     SEG_INITPOINT_CONTINUES)

         # A continuation from a prior segment

         ln -sv $WEST_PARENT_DATA_REF/seg.coor  ./parent.pdb

         ln -sv $WEST_PARENT_DATA_REF/seg.vel   ./parent.vel

         namd2 md-continue.conf > seg.out 

     ;;

 

     SEG_INITPOINT_NEWTRAJ)

         # Initiation of a new trajectory; $WEST_PARENT_DATA_REF contains the reference to the

         ln -sv seg_initial.pdb  ./parent.pdb 

         ln -sv seg_initial.vel     ./parent.vel 

         namd2 md-continue.conf > seg.out 

     ;;

 

     *)

         echo "unknown init point type $WEST_CURRENT_SEG_INITPOINT_TYPE"

         exit 2

     ;;

 esac

#Get pcoord

python rmsd_haziq.py > $WEST_PCOORD_RETURN

if [ -n "$SEG_DEBUG" ] ; then

    head -v $WEST_PCOORD_RETURN

fi

# Clean up

rm -f *.conf *.py  seg_restart.* *.prm *.temp *.pdb  *.psf

[Adam]

Hi Haziq,

This could be an unrelated error.  If something goes wrong during the actual simulation run, and not just the analysis phase, in runseg.sh, it'll fail to return a pcoord and display that error.

You should look at the output from a segment: seg_logs/000001-000000.log, for instance (or something along those lines).  It should contain more information about where the error is, specifically.  It sounds like your custom pcoord loader is working, so it might be more about the dynamics step.

Adam

---

Adam Pratt

Graduate Student in Chemistry

Chong Lab, Room 338, Eberly Hall

University of Pittsburgh

Pittsburgh, PA 15260

[Joshua Adelman]

Hi Haziq,

I think your problem is the following — your script, `rmsd_haziq.py` just loads `reference.pdb` and `seg_initial.pdb`, which are presumably the xtal structure and your initial basis/initial state coordinates. That’s fine, I think, to call in `get_pcoord.sh`, since the calculation is valid for determining the pcoord of your initial state. This mirrors what is being done in the scripts in the tutorial that you’re translating to use MDAnalysis (i.e. `get-rmsd-init.py`).

However, once you run a dynamic segment, you need to analyze the .dcd file produced by the the simulation in `runseg.sh`. Notice in the tutorial, there is a different python script called `get-rmsd.py`. This loads `seg.dcd`. Also be aware that `get-rmsd.py` lives in `auxfiles` and gets symbolically linked into the appropriate `traj_segs` directory in the line that reads:

ln -sv $WEST_SIM_ROOT/auxfiles/* .

So you need to put your script that processes a trajectory segment (the .dcd file), in `auxfiles` as well or add lines to the bash script that will makes sure it can be called with `runsegs.sh` runs. So work on writing a MDAnalysis equivalent of `get-rmsd.py` and I think that will move you in the right direction. It’s always good to test these scripts outside of a WESTPA run first so you can see what is going on without worrying about the more complex WESTPA setup. 

[Adam]

Whoops.  Missed that you'd posted the script. 

Thanks Josh.  Sorry Haziq!

Adam

---

Adam Pratt

Graduate Student in Chemistry

Chong Lab, Room 338, Eberly Hall

University of Pittsburgh

Pittsburgh, PA 15260

[Haziq Siddiqi]

Hi Josh and Adam,

Thank you for your help. Josh, I made the programs you recommended, but WESTPA is still not running smoothly.

Specifically, I replaced get-rmsd.py in both Auxfiles and the main director with a program that uses MDAnalysis to determine the RMSD from the .dcd file. I tested this program outside of WESTPA to confirm that it is able to calculate the RMSD. (code copied below)

However, when I run ./run.sh, I have the following error in west.log. My runseg.sh and get-rmsd.py are also copied below.

It seems like the error is with the shape of the progress coordinates. What can I do to resolve this problem?

Thank you! 

west.log

Maximum wallclock time: 125 days, 0:00:00

Wed Aug 10 13:04:16 2016

Iteration 1 (300 requested)

Beginning iteration 1

4 segments remain in iteration 1 (4 total)

1 of 59 (1.694915%) active bins are populated

per-bin minimum non-zero probability:       1

per-bin maximum probability:                1

per-bin probability dynamic range (kT):     0

per-segment minimum non-zero probability:   0.25

per-segment maximum non-zero probability:   0.25

per-segment probability dynamic range (kT): 0

norm = 1, error in norm = 0 (0*epsilon)

-- WARNING  [py.warnings] -- //anaconda/lib/python2.7/site-packages/numpy/lib/npyio.py:893: UserWarning: loadtxt: Empty input file: "/var/folders/fd/z56fbw1917l8ly588lvfbt8m0000gz/T/tmp1DMG69"

  warnings.warn('loadtxt: Empty input file: "%s"' % fname)

-- ERROR    [west.propagators.executable] -- could not read pcoord from '/var/folders/fd/z56fbw1917l8ly588lvfbt8m0000gz/T/tmp1DMG69': ValueError('progress coordinate data has incorrect shape (0, 1) [expected (2, 1)]',)

-- WARNING  [py.warnings] -- //anaconda/lib/python2.7/site-packages/numpy/lib/npyio.py:893: UserWarning: loadtxt: Empty input file: "/var/folders/fd/z56fbw1917l8ly588lvfbt8m0000gz/T/tmphDiGSz"

  warnings.warn('loadtxt: Empty input file: "%s"' % fname)

-- ERROR    [west.propagators.executable] -- could not read pcoord from '/var/folders/fd/z56fbw1917l8ly588lvfbt8m0000gz/T/tmphDiGSz': ValueError('progress coordinate data has incorrect shape (0, 1) [expected (2, 1)]',)

-- WARNING  [py.warnings] -- //anaconda/lib/python2.7/site-packages/numpy/lib/npyio.py:893: UserWarning: loadtxt: Empty input file: "/var/folders/fd/z56fbw1917l8ly588lvfbt8m0000gz/T/tmpUnVZn3"

  warnings.warn('loadtxt: Empty input file: "%s"' % fname)

-- ERROR    [west.propagators.executable] -- could not read pcoord from '/var/folders/fd/z56fbw1917l8ly588lvfbt8m0000gz/T/tmpUnVZn3': ValueError('progress coordinate data has incorrect shape (0, 1) [expected (2, 1)]',)

-- WARNING  [py.warnings] -- //anaconda/lib/python2.7/site-packages/numpy/lib/npyio.py:893: UserWarning: loadtxt: Empty input file: "/var/folders/fd/z56fbw1917l8ly588lvfbt8m0000gz/T/tmpTX8P0W"

  warnings.warn('loadtxt: Empty input file: "%s"' % fname)

-- ERROR    [west.propagators.executable] -- could not read pcoord from '/var/folders/fd/z56fbw1917l8ly588lvfbt8m0000gz/T/tmpTX8P0W': ValueError('progress coordinate data has incorrect shape (0, 1) [expected (2, 1)]',)

-- ERROR    [west.sim_manager] -- propagation failed for 4 segment(s):

0  

1  

2  

3

exception caught; shutting down

-- ERROR    [w_run] -- Traceback (most recent call last):

  File "/Users/haziq/Documents/westpa/westpa/lib/cmds/w_run.py", line 65, in <module>

    sim_manager.run()

  File "/Users/haziq/Documents/westpa/westpa/src/west/sim_manager.py", line 645, in run

    self.check_propagation()

  File "/Users/haziq/Documents/westpa/westpa/src/west/sim_manager.py", line 544, in check_propagation

    raise PropagationError('propagation failed for {:d} segments'.format(len(failed_segments)))

PropagationError: propagation failed for 4 segments

get-rmsd.py

from MDAnalysis import *

from MDAnalysis.analysis.align import *

from MDAnalysis.analysis.rms import rmsd

ref = Universe('chig.psf','reference.pdb')

mobile = Universe('chig.psf','seg.dcd')

for ts in mobile.trajectory:

rmsdval = rmsd(mobile.atoms.CA.positions, ref.atoms.CA.positions)

print "RMSD: ", rmsdval

portion of runseg.sh used to identify rmsd

#Get pcoord

python get-rmsd.py >& rmsd.temp 

wait

grep "RMSD: " rmsd.temp | gawk '{print $2}' | tail -2 > pcoord.dat

wait

cat pcoord.dat > $WEST_PCOORD_RETURN

get-rmsd-init.py

import MDAnalysis

from MDAnalysis.analysis.rms import rmsd

ref = MDAnalysis.Universe('chig.psf','reference.pdb')

seg = MDAnalysis.Universe('chig.psf','seg_initial.pdb')

ref_backbone = ref.select_atoms('backbone')

A = ref_backbone.positions.copy()

seg_backbone = seg.select_atoms('backbone')

B = seg_backbone.positions.copy()

output = rmsd(A,B, center=True)

print output

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[siddiqi...@gmail.com]

It appears that the issue is that WESTPA says my progress coordinate has the incorrect shape. I have copied the python program that calculates the PC, the script that calls this program, and WEST.log below. 

What can I do to resolve this problem? 

$ more get-rmsd.py

from MDAnalysis import *

from MDAnalysis.analysis.align import *

from MDAnalysis.analysis.rms import rmsd

ref = Universe('chig.psf','reference.pdb')

mobile = Universe('chig.psf','seg.dcd')

for ts in mobile.trajectory:

        rmsdval = rmsd(mobile.atoms.CA.positions, ref.atoms.CA.positions)

        print  rmsdval

        

$ more runseg.sh

python get-rmsd.py > $WEST_PCOORD_RETURN

if [ -n "$SEG_DEBUG" ] ; then

    head -v $WEST_PCOORD_RETURN

fi

# Clean up

rm -f *.conf *.py  seg_restart.* *.prm *.temp *.pdb  *.psf

$ more west.log

Maximum wallclock time: 125 days, 0:00:00

Fri Aug 12 13:19:28 2016

Iteration 1 (300 requested)

Beginning iteration 1

4 segments remain in iteration 1 (4 total)

1 of 59 (1.694915%) active bins are populated

per-bin minimum non-zero probability:       1

per-bin maximum probability:                1

per-bin probability dynamic range (kT):     0

per-segment minimum non-zero probability:   0.25

per-segment maximum non-zero probability:   0.25

per-segment probability dynamic range (kT): 0

norm = 1, error in norm = 0 (0*epsilon)

-- ERROR    [west.propagators.executable] -- could not read pcoord from '/var/folders/fd/z56fbw1917l8ly588lvfbt8m0000gz/T/tmpt2fQji': ValueError('progress coordinate data has incorrect shape () [expected (2, 1)]',)

-- ERROR    [west.propagators.executable] -- could not read pcoord from '/var/folders/fd/z56fbw1917l8ly588lvfbt8m0000gz/T/tmpDiKTXi': ValueError('progress coordinate data has incorrect shape () [expected (2, 1)]',)

-- ERROR    [west.propagators.executable] -- could not read pcoord from '/var/folders/fd/z56fbw1917l8ly588lvfbt8m0000gz/T/tmpJX6X2T': ValueError('progress coordinate data has incorrect shape () [expected (2, 1)]',)

-- ERROR    [west.propagators.executable] -- could not read pcoord from '/var/folders/fd/z56fbw1917l8ly588lvfbt8m0000gz/T/tmpyhLN4A': ValueError('progress coordinate data has incorrect shape () [expected (2, 1)]',)

-- ERROR    [west.sim_manager] -- propagation failed for 4 segment(s):

0  

1  

2  

3

exception caught; shutting down

-- ERROR    [w_run] -- Traceback (most recent call last):

  File "/Users/haziq/Documents/westpa/westpa/lib/cmds/w_run.py", line 65, in <module>

    sim_manager.run()

  File "/Users/haziq/Documents/westpa/westpa/src/west/sim_manager.py", line 645, in run

    self.check_propagation()

  File "/Users/haziq/Documents/westpa/westpa/src/west/sim_manager.py", line 544, in check_propagation

    raise PropagationError('propagation failed for {:d} segments'.format(len(failed_segments)))

PropagationError: propagation failed for 4 segments

[Joshua Adelman]

Hi Haziq,

It looks like your get-rmsd.py script isn’t returning any parseable values. You could set `SEG_DEBUG: 1` in your .cfg:

executable:
    environ: # environment variables for all executables
      SEG_DEBUG: 1

or just `cat` the `$WEST_PCOORD_RETURN` file. I’m guessing either the values aren’t being written to stdout or an error is occurring in the script. 

Josh

[Haziq Siddiqi]

Hi Josh,

Thanks for this message. You are correct that the issue is with my get-rmsd.py. To confirm this, when I replaced the get-rmsd.py script with a script that just outputs two integers, WESTPA is able to successfully run. So, WESTPA is working but I need to fix get-rmsd.py 

I am unable to use MDAnaylsis to read the seg.dcd. According to md-continue.conf, the output for each interval is a seg.dcd file. However, my current get-rmsd.py is not correctly able to open the seg.dcd. 

Currently, the line I am using to open seg.dcd is the following: 

u = MDAnalysis.Universe ('chig.psf','seg.dcd')

When working with a sample dcd file outside of WESTPA, this program works. But the issue I am having is I don't know how to get my get-rmsd.py to access the seg.dcd that is being generated by westpa at the end of each timestep. 

Where is the seg.dcd output stored? How can I access seg.dcd during my simulation from get-rmsd.py? 

Thank you!

[Joshua Adelman]

Hi Haziq,

A few notes:

- It seems strange to me that you are using md-continue.conf for point the initial segment and the continuation segment since typically two different configurations are required by NAMD having to do with setting the temperature initially from some random distribution vs using the temperature in the restart file that the simulation is continuing from. I’m wondering if NAMD is crashing before it creates seg.dcd. You should check to see if that file is there before the python script runs as a debugging step.

See:

https://github.com/westpa/westpa/blob/master/lib/examples/nacl_namd/westpa_scripts/runseg.sh#L22

vs

https://github.com/westpa/westpa/blob/master/lib/examples/nacl_namd/westpa_scripts/runseg.sh#L32

where the former using md-continue.conf and the latter uses md-genvel.conf

- At the start of runseg.sh, you execute the command `cd $WEST_CURRENT_SEG_DATA_REF`, which puts you into the proper directory within `traj_segs`. Everything in the script past that point assumes that the files are in that directory, unless otherwise specified using some other absolute or relative path. If you specify that the python script should look for “seg.dcd” it will assume that that file is in the working directory. 

Hope that helps.

Josh