From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Mon Nov 16 2015 - 08:42:08 CST
Hia Giacomo,
Thanks for the help!
Best regards,
Chitrak.
On Wed, Nov 11, 2015 at 12:00 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:
> I would just use the wall-time of a job as reference: if the queue system
> won't report it, just add a "date +%s" command to your script to get the
> time in seconds before and after running NAMD.
>
> Giacomo
>
> On Tue, Nov 10, 2015 at 9:18 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu>
> wrote:
>
>> Hi Giacomo,
>>
>> Thanks for your suggestion! I can now run the jobs.
>>
>> Is there a good way to benchmark the time it takes to run? Unlike a
>> regular NAMD job, this does not seem to be generating benchmark times on
>> its own.
>>
>>
>> Best regards,
>> Chitrak.
>>
>> On Fri, Nov 6, 2015 at 3:41 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
>> wrote:
>>
>>> Hello Chitrak: can you perhaps add to the replica.namd a Tcl check the
>>> presence of the file before executing NAMD? Something like an error
>>> message that gives you the replica number that is showing this error may
>>> help you dissect the problem.
>>>
>>> Giacomo
>>>
>>> On Thu, Nov 5, 2015 at 5:45 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> I am trying to work through the tutorial of replica exchange umbrella
>>>> sampling in NAMD. Somehow, I am getting the following error, although I do
>>>> have the colvars.conf file in the folder.
>>>>
>>>> colvars:
>>>> ----------------------------------------------------------------------
>>>> colvars: Initializing the collective variables module, version
>>>> 2014-10-23.
>>>> colvars:
>>>> ----------------------------------------------------------------------
>>>> colvars: Reading new configuration from file "colvars.conf":
>>>> colvars: Error: in opening configuration file "colvars.conf".
>>>> colvars: No such file or directory
>>>> colvars: If this error message is unclear, try recompiling with
>>>> -DCOLVARS_DEBUG.
>>>> FATAL ERROR: Error in the collective variables module: No such file or
>>>> directory
>>>> [0] Stack Traceback:
>>>>
>>>>
>>>>
>>>> Has anyone else faced this issue? I saw there was a bug regarding
>>>> loading colvars for restarting the simulation, but right now I am just
>>>> running the job0.conf file. Also, I am using NAMD 2.10
>>>>
>>>>
>>>> Best regards,
>>>> Chitrak.
>>>>
>>>
>>>
>>>
>>> --
>>> Giacomo Fiorin
>>> Assistant Professor of Research
>>> Institute for Computational Molecular Science (ICMS)
>>> College of Science and Technology, Temple University
>>> 1925 North 12th Street (035-07), Room 704D
>>> Philadelphia, PA 19122-1801
>>> Phone: +1-215-204-4213
>>> http://goo.gl/Q3TBQU
>>> http://giacomofiorin.github.io/
>>> https://icms.cst.temple.edu/members.html
>>>
>>>
>>>
>>
>
>
> --
> Giacomo Fiorin
> Assistant Professor of Research
> Institute for Computational Molecular Science (ICMS)
> College of Science and Technology, Temple University
> 1925 North 12th Street (035-07), Room 704D
> Philadelphia, PA 19122-1801
> Phone: +1-215-204-4213
> http://goo.gl/Q3TBQU
> http://giacomofiorin.github.io/
> https://icms.cst.temple.edu/members.html
>
>
>
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