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
> _______________________________________________
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--
-------------------------
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
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Received on Thu Dec 14 2017 - 10:30:03 PST
