4. PCA with CPPTRAJ#

 1#!/bin/bash
 2
 3module load ambertools23
 4
 5#sys="4ntds"
 6sys=$1
 7base="../1leader/${sys}"
 8init="step3_pbcsetup_1264"
 9atommask="@CA"
10n_vecs="10"
11
12results="pca1/${sys}"
13mkdir -p ${results}
14
15cpptraj <<_EOF
16parm ${base}/${init}.parm7
17trajin ${base}/prod??.nc
18rms first ${atommask}
19average crdset step3-average
20createcrd step3-trajectories
21run
22
23crdaction step3-trajectories rms ref step3-average ${atommask}
24crdaction step3-trajectories matrix covar name step3-covar ${atommask}
25
26runanalysis diagmatrix step3-covar out ${results}/step3-evecs.dat \
27vecs ${n_vecs} name myEvecs \
28nmwiz nmwizvecs ${n_vecs} nmwizfile ${results}/step3.nmd nmwizmask ${atommask} 
29
30run
31clear all
32
33readdata ${results}/step3-evecs.dat name Evecs
34
35parm ${base}/${init}.parm7
36parmstrip !(${atommask})
37parmwrite out ${results}/step3-mode.parm7
38
39runanalysis modes name Evecs trajout ${results}/step3-mode1.nc \
40pcmin -100 pcmax 100 tmode 1 trajoutmask ${atommask} trajoutfmt netcdf
41
42runanalysis modes name Evecs trajout ${results}/step3-mode2.nc \
43pcmin -100 pcmax 100 tmode 2 trajoutmask ${atommask} trajoutfmt netcdf
44
45_EOF

 1#!/bin/bash
 2
 3module load ambertools23
 4
 5#sys="4nt"
 6sys=$1
 7base="../1leader/${sys}"
 8init="step3_pbcsetup_1264"
 9atommask="@CA"
10n_vecs="10"
11
12results="pca2/${sys}"
13mkdir -p ${results}
14
15cpptraj <<_EOF
16parm ${base}ds/${init}.parm7 [ds]
17parm ${base}ov/${init}.parm7 [ov]
18
19trajin ${base}ds/prod??.nc parm [ds]
20trajin ${base}ov/prod??.nc parm [ov]
21
22rms first ${atommask}
23strip :WAT,Na+,Cl-,MG,DA5,DA,DA3,DT5,DT,DT3,DG5,DG,DG3,DC5,DC,DC3,
24average crdset step3-average
25createcrd step3-trajectories
26run
27
28crdaction step3-trajectories rms ref step3-average ${atommask}
29crdaction step3-trajectories matrix covar name step3-covar ${atommask}
30
31runanalysis diagmatrix step3-covar out ${results}/step3-evecs.dat \
32vecs ${n_vecs} name myEvecs \
33nmwiz nmwizvecs ${n_vecs} nmwizfile ${results}/step3.nmd nmwizmask ${atommask}
34run
35clear all
36
37readdata ${results}/step3-evecs.dat name Evecs
38
39parm ${base}ds/${init}.parm7
40parmstrip !(${atommask})
41parmwrite out ${results}/step3-mode.parm7
42
43runanalysis modes name Evecs trajout ${results}/step3-mode1.nc \
44pcmin -100 pcmax 100 tmode 1 trajoutmask ${atommask} trajoutfmt netcdf
45_EOF
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