From: Rana Rehan Khalid <rrkhalid.umich.edu>
Date: Thu, 14 Dec 2017 02:58:26 +0500

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
#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
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
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
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Received on Wed Dec 13 2017 - 14:00:02 PST
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