Re: Managing Log files

From: bo liu (liubo.njuer_at_gmail.com)
Date: Fri Sep 26 2008 - 22:01:40 CDT

Hi Navdeep,

How many timesteps do you set for the minimization?
minimization does output information every step, but this shouldn't bother
you because in most cases, a thousand steps of minimization is enough. I
think this wouldn't contribute to a very long .log file... In other cases,
more sophisticated protocol of minimization should be used, such as
alternating MD runs and Minimizations, rather than *too many* steps for
minimization at a time.

Regards,

2008/9/25 Nd S <navdeep79_at_gmail.com>

> Hi Alexander
>
> Is there any way out to reduce output information during minimization.
>
> Thanks
> Navdeep
>
>
> On Wed, Sep 24, 2008 at 1:01 PM, Alexander A. Vakhrushev <
> makaveli.lcf_at_gmail.com> wrote:
>
>> Hi Navdeep!
>> Perhaps your running minimization. In that case NAMD will still output
>> information in log file each step.
>>
>> 2008/9/24, Joshua Adelman <jadelman_at_berkeley.edu>:
>> > Hi Navdeep,
>> >
>> > That should work, and I've never seen it fail to. Is the problem that
>> the
>> > output files are still too long or is it that NAMD is really ignoring
>> the
>> > outputEnergies parameter?
>> >
>> > Josh
>> >
>> >
>> >
>> >
>> > On Sep 24, 2008, at 9:52 AM, Nd S wrote:
>> >
>> > Hi all
>> >
>> > While running a MD simulation in NAMD, the log file created is very
>> large as
>> > the energy values are stored at every step. I added the command
>> > "outputEnergies 5000" to output energy into stdout after every 5000
>> steps as
>> > per the NAMD manual, but it doesnt work. What's the other way out.
>> >
>> > Thanks
>> > Navdeep
>> >
>> >
>> >
>> ------------------------------------------------------------------------------------------------------
>> > Joshua L. Adelman
>> > Biophysics Graduate Group Lab: 510.643.2159
>> > 218 Wellman Hall Fax: 510.642.7428
>> > University of California, Berkeley
>> > http://nature.berkeley.edu/~jadelman
>> > Berkeley, CA 94720 USA jadelman_at_berkeley.edu
>> >
>> ------------------------------------------------------------------------------------------------------
>> >
>> >
>>
>>
>> --
>> Best regards,
>>
>> Dr. Alexander Vakhrushev
>> Institute of Applied Mechanics
>> Dep. of Mech. and Phys.-Chem.
>> of heterogeneous media
>> UB of Russian Academy of Sciences
>> 34 T. Baramzinoy St.
>> Izhevsk, Russia 426067
>> ----------------------------------
>> ӧѧا֧ߧڧ֧,
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>>
>> ..-.., ...
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>> ѧݧܧԧ է֧ݧ֧ߧڧ
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>> . . ѧѧާ٧ڧߧ 34
>> +7(3412)21-45-83
>>
>
>
>
> --
> --------------------------------------------
> Gig'em
> Navdeep Singh
>

-- 
-Liu bo
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