From: Douglas Houston (DouglasR.Houston_at_ed.ac.uk)
Date: Fri Mar 07 2014 - 08:55:47 CST
namd2 file.conf | tee file.log
This might make it easier to monitor exactly what is being written to
the file.
Quoting Ivan Gregoretti <ivangreg_at_gmail.com> on Fri, 7 Mar 2014
09:52:43 -0500:
> Hello Salvatore,
>
> I should have anticipated that response. Indeed, looking at the tail
> of the .log file is what I've been doing but the system is buffering
> the output in memory instead of writing to to the file.
>
> Perhaps this is an anomaly and the simulation crashed even though all
> processors continue working at full speed.
>
> Any thoughts?
>
> Ivan
>
>
>
>
> Ivan Gregoretti, PhD
> Bioinformatics
>
>
>
> On Fri, Mar 7, 2014 at 9:21 AM, Cosseddu, Salvatore
> <S.M.Cosseddu_at_warwick.ac.uk> wrote:
>> Dear Ivan,
>>
>> When you submit a calculation you usually use something like
>>
>> $ namd2 file.conf > file.log
>>
>> You you want to monitor the simulation you can just use
>>
>> $ tail -f file.log
>>
>> or
>>
>> $ less file.log
>>
>> and then press "F". If you want your output to be written more
>> often you can change output frequency parameters such as
>> outputEnergies.
>>
>> Regards
>> Salvatore
>>
>> ________________________________________
>> From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf
>> of Ivan Gregoretti <ivangreg_at_gmail.com>
>> Sent: 07 March 2014 14:08
>> To: namd-l_at_ks.uiuc.edu list
>> Subject: namd-l: Monitoring progress of an ongoing molecular
>> dynamics simulation
>>
>> Hello everybody,
>>
>> Could you share the way you monitor progress of an ongoing MD
>> simulation? ie What simulation step, roughly?
>>
>> We need to monitor progress using command line tools, not GUI. It
>> would be trivial with unix tools if the output weren't binary.
>>
>> I guess that a solution might involve VMD in text mode but all
>> suggestions are welcome.
>>
>> Thank you,
>>
>> Ivan
>>
>>
>>
>>
>>
>>
>> Ivan Gregoretti, PhD
>> Bioinformatics
>>
>
>
>
_____________________________________________________
Dr. Douglas R. Houston
Lecturer
Institute of Structural and Molecular Biology
Room 3.23, Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358
http://tinyurl.com/douglasrhouston
-- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:20:35 CST