Dear Sir
I reduced the number of trajectories files from the script. I ran the
script for 5 trajectories files it works and finish normally. I have total
12 mdcrd files. And I ran the PCA script 3 times now I have 3 .nc files and
three prmtop files. Can I combine these .nc file to analyze the histogram.
Kindly could you please guide me what changes i can made in the script as
you said """ Try doing it without creating a COORDS data set - this stores
all your coordinates in memory, which is convenient if you have the memory
to spare""" I want to check it too.
Kind Regards
On Thu, Dec 14, 2017 at 11:21 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Try doing it without creating a COORDS data set - this stores all your
> coordinates in memory, which is convenient if you have the memory to
> spare, but in this case you do not. This means you need to modify your
> coordinates each time you process them (i.e. you need to rms-fit
> before you project etc). Something like:
>
> # First run to generate average structure
> trajin bay_1.mdcrd
> ...
> rms first <mask>
> average crdset MyAverage
> run
> # Second run to generate covariance matrix and modes. Also run modes
> analysis.
> rms ref MyAverage <mask>
> matrix covar name bay1-covar <mask>
> diagmatrix bay1-covar name bay1-modes <options>
> modes name bay1-modes <options>
> run
> # Example third run for projection
> rms ref MyAverage <mask>
> projection MyProjection evecs bay1-modes <options>
>
> Hope this helps,
>
> -Dan
>
>
>
>
> On Wed, Dec 13, 2017 at 4:58 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
> wrote:
> > Dear Amber users
> >
> > I am trying to run the PCA script every time job stop due to this
> exceeded
> > limit of memory
> >
> > job 16802098 exceeded MEM usage hard limit (39282 > 2048)
> >
> > I use this script for running the job
> > #!/bin/bash
> > #PBS -l nodes=1:ppn=1
> > #PBS -l walltime=100:00:00
> > cd /nfs/amino-home/rrkhalid/bay60
> > /nfs/amino-library/local/Amber14/bin/cpptraj -p bay.prmtop -i
> pca.cpptraj
> >
> > and pca.cpptraj script is this each trajectory( 1-10 ) file run 750000
> > steps.
> > rajin bay_1.mdcrd
> > trajin bay_2.mdcrd
> > trajin bay_3.mdcrd
> > trajin bay_4.mdcrd
> > trajin bay_5.mdcrd
> > trajin bay_6.mdcrd
> > trajin bay_7.mdcrd
> > trajin bay_8.mdcrd
> > trajin bay_9.mdcrd
> > trajin bay_10.mdcrd
> > rms first :1-189&!.H=
> > average crdset average
> > createcrd avgtrajectories
> > run
> > crdaction avgtrajectories rms ref average :1-189&!.H=
> > crdaction avgtrajectories matrix covar name bay1-covar :1-189&!.H=
> > runanalysis diagmatrix bay1-covar out bay1-evecs.dat \
> > vecs 3 name myEvecs \
> > nmwiz nmwizvecs 3 nmwizfile bay.nmd nmwizmask :1-189&!.H=
> > ##########
> > clear all
> > readdata bay1-evecs.dat name Evecs
> > parm bay.prmtop
> > parmstrip !(:1-189&!.H=)
> > parmwrite out bay-modes.prmtop
> > runanalysis modes name Evecs trajout bay-mode1.nc \
> > pcmin -100 pcmax 100 tmode 1 trajoutmask :1-189&!.H= trajoutfmt netcd
> >
> > kindly guide Thanks
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Dec 14 2017 - 13:30:04 PST
