Re: [AMBER] cpptraj frames clustering limit

From: Gaurao Dhoke <dhokegaurav.gmail.com>
Date: Thu, 13 Aug 2015 10:28:01 +0200

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/




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Received on Thu Aug 13 2015 - 01:30:03 PDT
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