Thanks Dan,
It worked ..
Best :)
Tarique
>________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
>To: Syed Tarique Moin <tarisyed.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
>Sent: Saturday, January 12, 2013 7:26 PM
>Subject: Re: [AMBER] RMS2D
>
>Hi,
>
>What is the exact command you are using to run cpptraj? It seems like
>you might be running this in a parallel environment (like MPI; looks
>like maybe 4 threads?). Note that MPI is not supported for cpptraj;
>certain actions are OpenMP-enabled, but 2drms is not one of them yet.
>Also, based on the # of RMSDs to be calculated (739182025) you will
>need about 5.6 GB of free memory to successfully run the just the
>Rms2d command. By running in parallel, each thread is requesting 5.6
>GB so you may be blowing the system memory.
>
>Try running single-threaded, and potentially reduce the # of frames
>for which you're calculating 2drms (for example taking the RMSD of
>every other frame, 'trajin 1 last 2', should give you a similar
>picture and drastically reduce the amount of memory used).
>
>Hope this helps,
>
>-Dan
>
>On Sat, Jan 12, 2013 at 4:49 AM, Syed Tarique Moin <tarisyed.yahoo.com> wrote:
>> Hello,
>>
>>
>> AMBER users,
>>
>> I am trying to calculate RMS2D using cpptraj but getting no output and come up with following error. If anyone know, kindly help me out. I have re-compiled the amber package as following error says something like ...
>>
>> --------------------------
>> CTION OUTPUT:
>> RMS2D: Calculating RMSDs between each frame (739182025 total).
>> 0% 10% 10% 10% 10% 10% 10% 10% 10% 20% 20% 20% 20% 20% 20% 20% 20% 30% 30% 30% 30% 30% 30% 30% 30% 40% 40% 40% 40% 40% 40% 40% 40% 50% 50% 50% 50% 50% 50% 50% 60% 60% 60% 60% 60% 60% 70% 70% 70% 70% 70% 70% 80% 80% 80% 80% 80% 90% 90% 90% 90% 100% 100% 100% 100%
>> ===================================================================================
>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>> = EXIT CODE: 9
>> = CLEANING UP REMAINING PROCESSES
>> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>> ===================================================================================
>> YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9)
>> This typically refers to a problem with your application.
>> Please see the FAQ page for debugging suggestions
>> -------------------------------------------------------------------------
>>
>> The syntax for the rms2d, I used is as follows..
>> ----------
>> rms2d first rmsout comt-backbone.rms2d.gnu .C,CA,N time 1
>> --------------
>>
>> Thanks in advance
>> Regards
>>
>> Tarique
>>
>>
>>
>> -----------------------------
>> Syed Tarique Moin, Ph.D.
>> Post Doctoral Fellow,
>>
>> Institute of General, Inorganic and Theoretical Chemistry
>> Center for Chemistry and Biomedicine
>> University of Innsbruck
>> Innrain 80-82
>> A-6020 Innsbruck
>> AUSTRIA
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>--
>-------------------------
>Daniel R. Roe, PhD
>Department of Medicinal Chemistry
>University of Utah
>30 South 2000 East, Room 201
>Salt Lake City, UT 84112-5820
>http://home.chpc.utah.edu/~cheatham/
>(801) 587-9652
>(801) 585-9119 (Fax)
>
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>
>
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Received on Mon Jan 14 2013 - 02:30:02 PST
