AMBER Archive (2006)

Subject: AMBER: Problems with equilibrating the starting density

From: Markus Weingarth (M.Weingarth_at_web.de)
Date: Fri Nov 03 2006 - 11:32:20 CST

Hello, I would like to equilibrate the densitiy of my starting state. I operate with PBC and a waterbox.
I recived a script from one of our group - she ment it should be sufficient for my demands: Anyway, I don't get it to start it.

This is my script

# druckk
cat > ddrug011.in << schluss
Titel
 &cntrl
  imin=0, irest=0, ntx=1,
   ntt=1, temp0=300.0, tautp=1.0, taup=0.5,
   ntb=2, ntp=2,
   cut=20,
   ntc=1, ntf=1,
   iwrap=0,
   nstlim=35000,
   ntwe=35001, ntwx=100, ntpr=100,
   ntwr=100,
   ntwprt=0,
  &end
  &wt
   type='END'
  &end
schluss
/d2/amber8/amber8/exe/sander \
 -O -i ddrug011.in -o ddrug011.out -p drug011.top \
  -c drug011.rst -x ddrug011.trj -inf ddrug011.inf \
   -r ddrug011.rst -ref drug011.rst

cat > dkdrug011.in << schluss
Titel
 &cntrl
  imin=0, irest=0, ntx=1,
   ntt=1, tempi=300.0, temp0=300.0,
   ntb=0, ntp=0,
   cut=20,
   ntc=1, ntf=1,
   iwrap=0,
   nstlim=35000,
   ntwe=35001, ntwx=100, ntpr=100,
   ntwr=100,
   ntwprt=0,
  &end
  &wt
   type='END'
  &end
schluss
/d2/amber8/amber8/exe/sander \
 -O -i dkdrug011.in -o dkdrug011.out -p drug011.top \
  -c ddrug011.rst -x dkdrug011.trj -inf dkdrug011.inf \
   -r dkdrug011.rst -ref ddrug011.rst

cat > kdrug011.in << schluss
Titel
 &cntrl
  imin=0, irest=1, ntx=5,
   ntt=0, tempi=300.0,
   ntb=0, ntp=0,
   cut=20,
   ntc=1, ntf=1,
   iwrap=0,
   nstlim=100000,
   ntwe=100001, ntwx=100, ntpr=100,
   ntwr=100,
   ntwprt=0,
  &end
  &wt
   type='END'
  &end
schluss
/d2/amber8/amber8/exe/sander \
 -O -i kdrug011.in -o kdrug011.out -p drug011.top \
  -c ddrug011.rst -x kdrug011.trj -inf kdrug011.inf \
   -r kdrug011.rst -ref ddrug011.rst

The error has to be (at least I think so) in the first part

# druckk
cat > ddrug011.in << schluss
Titel
 &cntrl
  imin=0, irest=0, ntx=1,
   ntt=1, temp0=300.0, tautp=1.0, taup=0.5,
   ntb=2, ntp=2,
   cut=20,
   ntc=1, ntf=1,
   iwrap=0,
   nstlim=35000,
   ntwe=35001, ntwx=100, ntpr=100,
   ntwr=100,
   ntwprt=0,
  &end
  &wt
   type='END'
  &end
schluss
/d2/amber8/amber8/exe/sander \
 -O -i ddrug011.in -o ddrug011.out -p drug011.top \
  -c drug011.rst -x ddrug011.trj -inf ddrug011.inf \
   -r ddrug011.rst -ref drug011.rst

- without that part, I am able to start the calculation. Actually, this

/d2/amber8/amber8/exe/sander \
 -O -i ddrug011.in -o ddrug011.out -p drug011.top \
  -c drug011.rst -x ddrug011.trj -inf ddrug011.inf \
   -r ddrug011.rst -ref drug011.rst

should also be correct ( I copied the settings for the MD with constant temperatur and it worked).

I am really a bit desperated because me and especially my much more amber-experienced group can't find the problem.

this is the nohup.out :

./sdk1b: line 23: 21909 Getötet /d2/amber8/amber8/exe/sander -O -i ddrug011.in -o ddrug011.out -p drug011.top -c drug011.rst -x ddrug011.trj -inf ddrug011.inf -r ddrug011.rst -ref drug011.rst
PGFIO-F-217/list-directed read/unit=9/attempt to read past end of file.
 File name = fort.9 formatted, sequential access record = 1
 In source file _ew_box.f, at line number 1745
PGFIO-F-217/list-directed read/unit=9/attempt to read past end of file.
 File name = fort.9 formatted, sequential access record = 1
 In source file _ew_box.f, at line number 1745

additional info :

If I try to start the job, the ddug011.in and the dkdrug011.in are written, and thats all. (calculation stops but samder still runs....bit strange)

would anyone be so kind to help me or give me a hint?

Hopefully,

Markus Weingarth

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