AMBER Archive (2008)

Subject: Re: AMBER: problems with restart of MD

From: Vijay Singh (vijayratan.singh_at_gmail.com)
Date: Fri Jan 11 2008 - 14:04:39 CST

Hi,

   Thanks for the response. I actually tried NTX = 5 too. Result was same as
that with NTX=7. But, I will go ahead and try once again and may be wait a
little more longer to see if the output file updates properly.

Thanks again,
Vijay

On Jan 11, 2008 2:56 PM, Ross Walker <ross_at_rosswalker.co.uk> wrote:

> 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
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
> ------------------------------
> *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
>
> ----------------------------------------------------------------------------
> ----
> 3. ATOMIC COORDINATES AND VELOCITIES
> ----------------------------------------------------------------------------
> ----
>
>
> Could someone please help me on that.
>
> Regards
> Vijay
>
>

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