Re: [AMBER] problem of ptraj

From: fancy2012 <fancy2012.yeah.net>
Date: Mon, 27 Dec 2010 11:28:30 +0800 (CST)

Hi Dr. Dan,
Thanks very much for your reply. The version of AmberTools is 1.2, and of course I have applied all the bugfixes. The attached files are input and output files for the analysis. And I also checked the output file, but there was not any error. Hoping that you can figure it out. Thank you again.



At 2010-12-21úČ"Daniel Roe" <daniel.r.roe.gmail.com> wrote:

>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 2010-12-20úČ"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
>>>> _______________________________________________
>>>> 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

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber



Received on Sun Dec 26 2010 - 19:30:02 PST
Custom Search