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createremddirs's Issues

Issue understanding the logic of the program

Sorry if I'm missing something obvious,

I want to test this software but I'm having problems creating the input directories. I want to do Parallel Tempering, and have generated the temperature list with an automatic generator. I have stored the temperatures in the Temperature.dat file, containing in total 263 temperatures.

My remd.opts is set up like so:

DIMENSION   Temperatures.dat
NSTLIM      500
NUMEXCHG    100
TOPOLOGY    /Users/je714/test_createRMDdirs/top.prmtop
CRD_FILE    /Users/je714/test_createRMDdirs
MDIN_FILE   pme.remd.in
FULLARCHIVE 0

I've tried changing the CRD_FILE variable from /Users/je714/test_createRMDdirs with /Users/je714/test_createRMDdirs/inpu_coords.inpcrd but it makes no difference.

And my pme.remd.in file is the following:

  ntwx = 5000
 ioutfm = 1,
 ntwr = 100000,
 ntxo = 2,
 ntpr = 5000,
 iwrap = 1,
 ntc = 2,
 ntf = 2,
 cut = 8.0,
 ntt = 3,
 gamma_ln = 1,
 dt = 0.004,
 ig = -1,
 ntb=2,
 ntp=1,
 barostat=2,

Now I use CreateRemdDirs to setup 10 runs but I get the following error:

$ CreateRemdDirs -b 0 -e 10

CreateRemdDir: Amber run input creation/job submission/job check.
Version: 0.9b
Daniel R. Roe, 2015
  START            : 0
  STOP             : 10
Working Dir: /Users/je714/test_createRMDdirs
Reading input from file: remd.opts
    Dim 1: Temperature exchange from 300 K to 500.48 K (263)
  MDIN_FILE        : pme.remd.in
  NSTLIM=500, DT=-1.000000
  NUMEXCHG=100
  CRD_DIR          : /Users/je714/test_createRMDdirs/inputcrd.inpcrd
  1 dimensions, 263 total replicas.
Creating 11 runs from 0 to 10
  RUNDIR: run.000
    Run 0: irest=0, ntx=1
Error: Coords /Users/je714/test_createRMDdirs/inputcrd.inpcrd/001.rst7 not found.

It does create a run.000 directory with the following content though:

$ tree run.000/
run.000/
├── [ 102]  INPUT
│   └── [ 367]  in.001
└── [   0]  groupfile

1 directory, 2 files

What am I doing wrong? Why haven't the other directories been created?

I've asked here rather than in the AMBER mailing list as it seems this is still in development and there's no info about this software in the manual.

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