Re: [AMBER] problem of ptraj

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Mon, 20 Dec 2010 11:40:42 -0500

Hi,

The exact nature of your problem is still not clear. Please attach
what output ptraj produces when the problem occurs. Also, what version
of AmberTools are you using, and have you applied all of the bugfixes
(http://ambermd.org/bugfixesat.html)? In particular, bugfix 16 deals
specifically with ptraj and large coordinate files.

-Dan

2010/12/20 fancy2012 <fancy2012.yeah.net>:
> 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 2010-12-20´╝î"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
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>>--
>>Jason M. Swails
>>Quantum Theory Project,
>>University of Florida
>>Ph.D. Graduate Student
>>352-392-4032
>>_______________________________________________
>>AMBER mailing list
>>AMBER.ambermd.org
>>http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Dec 20 2010 - 09:00:02 PST
Custom Search