AMBER Archive (2006)

Subject: AMBER: proper restart procedure?

From: John J. Love (jlove_at_sciences.sdsu.edu)
Date: Tue May 02 2006 - 22:33:57 CDT

Hello Amber Users,
 
I have tried to find a solution to the current problem I'm having in a
number of places but I have not been successful. I believe this is a
simple problem. I am having no success in restarting MD runs after an
unplanned stop (crash). I have looked in the manuals, tutorials,
archives, threads, etc. and have not found a solution. If you know of a
reference source to solve this please let me know.
 
The original sander command -
 
$AMBERHOME/exe/sander -O -i W43Y_GB_md1.in -o W43Y_GB_md1.out -c
W43Y_GB_init_min.rst -p W43Y.prmtop -r W43Y_GB_md1.rst -x
W43Y_GB_md1.mdcrd
 
This is the original input file -
(Before)
10-mer DNA MD
&cntrl
  imin = 0, ntb = 0,
  igb = 1, ntpr = 100, ntwx = 100,
  ntt = 1, gamma_ln = 1.0,
  tempi = 300.0, temp0 = 300.0,
  nstlim = 1500000, dt = 0.001,
  cut = 12
 /
 
After the crash I have modified the input file as such
(W43Y_GB_md1_rst.in) -
(After)
10-mer DNA MD
 &cntrl
  imin = 0, irest=1, ntx=7, ntb = 0,
  igb = 1, ntpr = 100, ntwx = 100,
  ntt = 1, gamma_ln = 1.0,
  tempi = 300.0, temp0 = 300.0,
  nstlim = 1500000, dt = 0.001,
  cut = 12
 /
 
I then run the following command -
$AMBERHOME/exe/sander -O -i W43Y_GB_md1_rst.in -o W43Y_GB_md1_rst.out -c
W43Y_GB_md1.rst -p W43Y.prmtop -r W43Y_GB_md1_rst.rst -x
W43Y_GB_md1_rst.mdcrd
 
The program exits very quickly and I get this in the tail of the output
file (W43Y_GB_md1_rst.out) -
------------------------------------------------------------------------
--------
   3. ATOMIC COORDINATES AND VELOCITIES
------------------------------------------------------------------------
--------
 
 
     rfree: End of file on unit 9
 
 
If anyone could tell me what I'm doing wrong I'd appreciate it.
 
thanks,
John Love
 
 
 
 
John J. Love
Chemistry and Biochemistry Department
San Diego State University
San Diego, CA 92182-1030
619-594-2063
http://www.chemistry.sdsu.edu/faculty/Love/
 

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