First, you're running with an out-of-date version of cpptraj (14.05).
Update to version 15 (free with AmberTools 15).
Second, I recommend trying out the 'loadtraj' command like I suggested
previously to save some memory. You also may need to use the 'sieve'
keyword to reduce the size of the pairwise distance matrix (also
previously suggested).
Hope this helps,
-Dan
On Thu, Aug 13, 2015 at 2:28 AM, Gaurao Dhoke <dhokegaurav.gmail.com> wrote:
> Dear all,
> Thank you for your valuable suggestions.
> Here are the input and the log file that i got from cpptraj.
> I m trying to run cpptraj jobs in parallel and using cpptraj with mpi.
> As my topology file for all trajectory is same so I even tried with
> 'loadcrd' but the error is same.
> I really don't know what is the problem?
> Thank you.
>
>
>
>
> On 12 August 2015 at 17:06, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> On Wed, Aug 12, 2015 at 9:46 AM, Gaurao Dhoke <dhokegaurav.gmail.com>
>> wrote:
>> > I have found that cpptraj is not able to process long trajectory for
>> > analysis.
>>
>> It would help if you could provide more information on what you mean
>> here. Does cpptraj print a warning/error message? Does it crash?
>>
>> On Wed, Aug 12, 2015 at 7:59 AM, Jason Swails <jason.swails.gmail.com>
>> wrote:
>> > On Wed, Aug 12, 2015 at 9:46 AM, Gaurao Dhoke <dhokegaurav.gmail.com>
>> wrote:
>> >> Is there any way to increase this limit?
>> >
>> > Since you're doing clustering, either your system is running out of
>> memory
>> > or you are expecting a calculation that may take hours or days to finish
>> > much faster than that (so you think it's hanging, when in fact it's still
>> > working). You haven't provided enough information about what happened
>> for
>> > me to know for sure.
>> >
>> > If you are actually running out of memory, your choices are either use a
>> > machine that has more RAM, or use the "sieve" option, which will generate
>> > the clusters based on a reduced number of frames, and then assign *all*
>> of
>> > the frames to that cluster. More details are available in the manual.
>>
>> There is actually a third option - you can use the 'loadtraj' command
>> to load your frames as a trajectory (TRAJ) data set, which functions
>> like a coordinates (COORDS) data set except everything is kept
>> on-disk. The 'loadtraj' command can be used to make a TRAJ data set
>> out of existing 'trajin' entries, or can be used to load a trajectory
>> separately. The only limitation is that all trajectories in a TRAJ
>> data set must correspond to the same topology file. So you could do
>> for example:
>>
>> parm myparm.parm7
>> trajin traj1.nc
>> trajin traj2.nc
>> loadtraj name crd1
>> cluster crdset crd1 <more cluster options>
>>
>> See the Amber 15 manual section 29.4 for more on using coordinates as
>> data sets in cpptraj. Note that you will still need enough memory to
>> store the pairwise distance matrix, so you may need to use the 'sieve'
>> option as well depending on how much memory you have available.
>>
>> Hope this helps,
>>
>> -Dan
>>
>> >
>> > Also, I would highly recommend upgrading to AmberTools 15 if you haven't
>> > already (if you have Amber 14, you can do this with a simple
>> > "./update_amber --upgrade" command).
>> >
>> > HTH,
>> > Jason
>> >
>> > --
>> > Jason M. Swails
>> > BioMaPS,
>> > Rutgers University
>> > Postdoctoral Researcher
>> > _______________________________________________
>> > 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 307
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
>
> ------------------------------------------------------------------
>
> *With kind regards,*
>
> *Gaurao Dhoke*
>
> PhD Scholar
>
> Room No. 4.141
>
> Institute of Biotechnology
> RWTH Aachen University
> Worringerweg 3, 52074 Aachen
> Germany
>
> Mobile: +4917684171309
> Office Phone: +49-241-80-23603
> Homepage: www.biotec.rwth-aachen.de
>
>
> Personal Website: http://gauraovdhoke.webs.com/
>
> _______________________________________________
> 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 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 13 2015 - 12:00:06 PDT
