Hi Vijay,
Check out the irest option. If you need to restart after first MD run, I
think you need to use irest=1 and not zero.
Senior members can suggest if there is anything else wrong.
Hope this helps.
Cheers
PanDa
===============================================================
If your ship doesn't come in, swim out to it...Jonathan Winters
===============================================================
Pankaj R. Daga |
Dept. of Medicinal Chemistry | e-mail: pdaga_at_olemiss.edu
417 Faser Hall, | fax: +1-662-915-5638
University of Mississippi | phone: +1-662-915-1853
University, MS, 38677-1848 |
===============================================================
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Vijay Singh
Sent: Friday, January 11, 2008 11:30 AM
To: amber.scripps.edu
Subject: AMBER: problems with restart of MD
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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Received on Sun Jan 13 2008 - 06:07:26 PST
