AMBER Archive (2008)

Subject: Re: AMBER: problems with restart of MD

From: Age.Skjevik_at_student.uib.no
Date: Fri Jan 11 2008 - 12:16:00 CST

Hello!

It seems like you have forgot to include tempi=800.0 in the second
input file, if you're thinking of keeping the temperature at 800 K.

Regards,

Åge Skjevik

Siterer Vijay Singh <vijayratan.singh_at_gmail.com>:

> 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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