From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Mar 17 2014 - 02:22:26 CDT
the final portion of the conf file reads
# output
outputName ./nvt_accel_03
outputEnergies 500 ;# multiple of fullElectFrequency or viceversa
restartfreq 100
DCDfreq 500
binaryrestart yes
binaryoutput no
# wrapNearest no
# wrapAll on
seed 313131
run 10000000
This time (without changing the conf file) it performed correctly
francesco
On Sun, Mar 16, 2014 at 9:58 PM, Aron Broom <broomsday_at_gmail.com> wrote:
> do you need the run command? Or could you just use timesteps?
>
>
> On Sun, Mar 16, 2014 at 3:57 PM, Francesco Pietra <chiendarret_at_gmail.com>wrote:
>
>> However, on next attempt, with same files, same problem as initially
>> posted, with or without the ++verbose option.
>> fp
>>
>> ---------- Forwarded message ----------
>> From: Francesco Pietra <chiendarret_at_gmail.com>
>> Date: Sun, Mar 16, 2014 at 8:48 PM
>> Subject: Fwd: TCL command "run" erratic
>> To: NAMD <namd-l_at_ks.uiuc.edu>
>>
>>
>> Now, after a very large number of failed attempts by changing command, by
>> adding the "++verbose" option to the command line, the requested number of
>> steps were carried out
>> fp
>>
>>
>> ---------- Forwarded message ----------
>> From: Francesco Pietra <chiendarret_at_gmail.com>
>> Date: Sun, Mar 16, 2014 at 8:40 PM
>> Subject: TCL command "run" erratic
>> To: NAMD <namd-l_at_ks.uiuc.edu>
>>
>>
>> Hellow:
>> From time to time, with all my shared-mem computers, either CPU or
>> CPU-GPU, and binary namd2.9, I am faced by erratic behavior of the "run"
>> command. Here with a minimal CPU computer based on dual-opteron (for
>> MacCammon acceleratedMD under Case GB conditions):
>>
>> ..........................................
>> .........................................
>> colvars: Collective variables module initialized.
>> colvars:
>> ----------------------------------------------------------------------
>> Info: useSync: 1 useProxySync: 0
>> Info: Startup phase 8 took 0.018353 s, 120.816 MB of memory in use
>> Info: Startup phase 9 took 0.000530005 s, 120.816 MB of memory in use
>> Info: Startup phase 10 took 0.000347972 s, 121.281 MB of memory in use
>> Info: Finished startup at 0.119451 s, 121.281 MB of memory in use
>>
>> TCL: Running for 10000 steps
>> francesco_at_tya64:~/tmp/accelMD$
>>
>> This also occurs with conf file that a few hours ago led to the "run"
>> command behaving regularly.
>>
>> Any suggestion?
>> Thanks
>> francesco pietra
>>
>>
>>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>
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