Hi Bingwu,
Can you take a look at the restart file and let us know if you see a
bunch of entries that look like "******" instead of numbers? Given
the length of your simulation and the fact that you are not using
iwrap to "wrap" the coordinates, it is quite possible that some of the
coordinates in your system have exceeded 999 Å from the origin and are
not being written out properly in the restart file.
I would also recommend cleaning up your input script. If you are
really running a simple NPT simulation, then at least a few of the
parameters you have are redundant (since many of them are defaults) or
unnecessary. For instance, I don't see why you need nmropt = 1 or any
of the temperature section (since you aren't do annealing). I would
suggest the following:
> Dynamic Simulation with Constant Pressure
> &cntrl
> imin = 0, irest = 1, ntx = 5,
> iwrap = 1, ntb = 2,
> ntr = 0, ntc = 2, ntf = 2, cut = 8.0,
> ntt = 1, temp0 = 300.0, tempi = 300.0, tautp = 1.0,
> ntp = 1, taup = 0.1, comp = 44.6, pres0 = 1.0,
> nstlim = 100000000, dt = 0.002,
> ntwx = 500, ntpr = 500, ntwr = 500000,
> /
A few other things to consider:
(1) Do you really want the Berendsen thermostat (ntt = 1)? If you
want to generate a "true" NPT trajectory, you might want to switch to
Andersen (ntt = 2) or Langevin (ntt = 3) thermostats.
(2) You might also want to explicitly define the frequency of restart
files (using ntwr, as in the above example) because it otherwise
defaults to 500, which is probably too frequent.
(3) The pressure coupling is quite "tight". You might want to
increase taup to something on the order of 1.0-5.0 unless there is a
good reason to have it so short.
Best,
Paul
On Sep 27, 2010, at 10:41 AM, Yu, Bingwu wrote:
> Hi All,
>
> I need to run a 1 us amber simulation. To avoid possible problem
> during the runs, I decide to run one 200 ms experiment first then
> restart it with another 200 ms. The 1st simulation is done. But I
> can not start the 2nd 200 ms as a restart experiment.
>
> error says:
>
> lib-4190 : UNRECOVERABLE library error
> Unable to find error message (check NLSPATH, file lib.cat<http://lib.cat
> >)
>
> Encountered during a sequential formatted READ from unit 9
> Fortran unit 9 is connected to a sequential formatted text file:
> "md_out.rst"
> Current format: 9028 FORMAT(6f12.7)
> ^
> kill 3149: No such process
> kill 3176: No such process
> kill 3316: No such process
> ~
>
> Here is md_restart.in<http://md_restart.in> :
>
> Dynamic Simulation with Constant Pressure
>
> # Control section
> &cntrl
> ntwx = 500, ntpr = 500,
> ntt = 1, temp0 = 300.0, tempi = 300.0, tautp = 1.0,
> scnb = 2.0, scee = 1.2, dielc = 1, cut = 8.0,
> ntb = 2, ntc = 2, ntf = 2,
> nstlim = 100012000, dt = 0.0020,
> ntp = 1, taup = 0.1, comp = 44.6, pres0 = 1.0,
> ibelly = 0, ntr = 0,
> imin = 0, irest = 1, ntx = 5, nmropt = 1,
> /
> &ewald
> skinnb = 2.0,
> nbflag = 1,
> /
>
> &wt
> type = 'TEMP0', istep1 = 1, istep2 = 100012000, value1 = 300.0,
> value2 = 300.0,
> /
> &wt
> type='END'
> /
> END
>
> Please advise. thanks!
>
> Bingwu
>
>
>
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Received on Mon Sep 27 2010 - 11:30:07 PDT
