AMBER Archive (2008)

Subject: RE: AMBER: problems with restart of MD

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Jan 11 2008 - 13:56:16 CST

Hi Vijay,
 
The issue is that you are running a non-periodic simulation here (ntb=0) but
when you restart you are setting ntx=7 which tells sander to expect box
information from the input coordinate file. Since your input coordinate file
does not have any box info the code is hanging there waiting for that
information to be appended to the file. I realize we should probably find a
better way to do this in the code so it fails gracefully rather than just
hanging but this isn't always easy in parallel.
 
Anyway, to answer your problem set ntx=5 and everything should be good. Also
note that with Amber 9 you can always set NTX=5 and it will auto load the
box info if you are running a periodic simulation. Thus ntx=7 is actually
deprecated as an option hence why it is no longer in the manual.
 
All the best
Ross

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From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Vijay Singh
Sent: Friday, January 11, 2008 09:30
To: amber_at_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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