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License: GNU General Public License v2.0
Automatically generate input for running M-REMD simulations (and more) in Amber.
License: GNU General Public License v2.0
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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