Re: Managing Log files

From: Nd S (navdeep79_at_gmail.com)
Date: Fri Sep 26 2008 - 22:55:24 CDT

Hi Liubo

I am usually going for approximately 10000 steps of minimization. For large
systems I am facing a problem as it takes hell lot of time. I have to do
this as usually my starting geometry is in pretty bad shape. Can you please
explain to me the strategy you mentioned.

Thanks
Navdeep

2008/9/26 bo liu <liubo.njuer_at_gmail.com>

> 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
>>> ----------------------------------
>>> С уважением,
>>> Вахрушев Александр Александрович
>>>
>>> к.ф.-м.н., с.н.с.
>>> Институт прикладной механики
>>> Уральского Отделения
>>> Российской Академии Наук
>>> 426067, г. Ижевск
>>> ул. Т. Барамзиной 34
>>> +7(3412)21-45-83
>>>
>>
>>
>>
>> --
>> --------------------------------------------
>> Gig'em
>> Navdeep Singh
>>
>
>
>
> --
> -Liu bo
> -----------------------------------------------------------
> Computational Biochemistry&Biophysics, Nano-bio systems: MD method;
> College of Chemistry and Chemical Engineering, Graduate University of
> Chinese Academy of Sciences, Beijing P.R. China
> Office: (86)-010-88233187
> Home: (86)-010-88259765
> Cell: 13426057875
>

-- 
--------------------------------------------
Gig'em
Navdeep Singh

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:49:53 CST