Re: [AMBER] problem of ptraj

From: fancy2012 <fancy2012.yeah.net>
Date: Mon, 20 Dec 2010 18:32:55 +0800 (CST)

Hi Jason Swails,
 
Thanks very much for your reply and explanation. When I did ptraj analysis, there was no error, but the mdcrd files could not be read in. For example, mdcrd files of 100ps heating, 100ps density equilibration and 250ps equilibration
of NPH could be read in, but mdcrd files of 1000ps production at NPH could not be read in. Each production file is about 3~4 GB, so I am thinking that may be a problem of the size of the file. Could you give me some other suggestion? Thanks very much!

Best wishes,

Qinghua Liao

Ph.D student of Tianjin University, China




At 2010-12-20úČ"Jason Swails" <jason.swails.gmail.com> wrote:

>On Sun, Dec 19, 2010 at 9:54 PM, fancy2012 <fancy2012.yeah.net> wrote:
>
>> Hi amber users,
>>
>> There is a problem for me to use ptraj to analyse. The single file of
>> *.mdcrd is too big to be read in by ptraj, Does
>
>
>How do you know it is "too big"? Nowadays, a *too-big* mdcrd file would
>have to be simply massive as operating systems, filesystems, and
>architecture have caught up to the demands of large file support.
>
>What errors do you get?
>
>It's possible that a different compilation on a 64-bit OS would be able to
>fix this if it is indeed a file size related problem.
>
>All the best,
>Jason
>
>somebody have some effective methods to deal with such problem? Thanks very
>> much!
>>
>> Best wishes,
>>
>> Qinghua Liao
>>
>> Ph.D student of Tianjin University, China
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
>--
>Jason M. Swails
>Quantum Theory Project,
>University of Florida
>Ph.D. Graduate Student
>352-392-4032
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Received on Mon Dec 20 2010 - 03:00:02 PST
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