AMBER Archive (2008)

Subject: AMBER: problems with restart of MD

From: Vijay Singh (vijayratan.singh_at_gmail.com)
Date: Fri Jan 11 2008 - 11:29:31 CST

Hi,

Not sure if my messages are reaching the right destination. I did not get
any response on 2 different occasions earlier. Neverthless, another try.

I am using amber9 and doing some very basic MD.I am having some trouble with
the restart of MD production run. Not sure where I am going wrong. After
initial minimization, the first part of run is fine

The input files looks -

&cntrl
 imin = 0, ntb = 0, irest = 0,
 igb = 1, ntpr = 10000, ntwx = 1000,
 ntt = 3, gamma_ln = 1.0,
 temp0 = 800.0,tempi = 800.0,
 nstlim = 40000000, dt = 0.001,
 cut = 999
/

mpiexec $AMBERHOME/exe/sander.MPI -O -i md_800k_1.in -o md800_1.out -c
t57c_min.rst -p t57c.prmtop -r mdout800_1.rst -x mdout800_1.mdcrd

   Till this point I get all the output as needed. But the 2nd step below is
where I get stuck on the restart part, the input is as follows -

&cntrl
 imin = 0, ntb = 0, irest = 1, ntx = 7,
 igb = 1, ntpr = 10000, ntwx = 1000,
 ntt = 3, gamma_ln = 1.0,
 temp0 = 800.0,
 nstlim =40000000, dt = 0.001,
 cut = 999
/

 #mpiexec $AMBERHOME/exe/sander.MPI -O -i md_800k_2.in -o md800_2.out -c
mdout800_1.rst -p t57c.prmtop -r mdout800_2.rst -x mdout800_2.mdcrd

  From here I don't get any output. The mdout file stops with -

Langevin dynamics temperature regulation:
   ig = 71277
   temp0 = 800.00000, tempi = 0.00000, gamma_ln= 1.00000
| INFO: Old style inpcrd file read

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3.  ATOMIC COORDINATES AND VELOCITIES
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Could someone please help me on that.

Regards
Vijay

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