HI,
yes that is correct you will get 200 frames.
Best Regards
Elvis Martis
Mumbai, INDIA.
________________________________________
From: Thakur, Abhishek <axt651.miami.edu>
Sent: 14 July 2017 03:16:25
To: amber.ambermd.org
Subject: [AMBER] PCA - first mode of motion
Hi everyone,
I am doing PCA analysis to get the first mode of motion over 100ns of tajectory, but while examining the video on VMD I can see only 201 frames.
I am new to it, I want to know is this usual or something is wrong. As I am giving 10ns trajectory as an input for PCA analysis.
Here is what I am following:
trajin /projects/chem/ionic/abhi/A_114/NEW_analysis/cluster/AI/TEST/A-114_prod_0-100ns.crd.gz
rms first :1-462&!.H=
average crdset cpu-gpu-average
createcrd cpu-gpu-trajectories
run
crdaction cpu-gpu-trajectories rms ref cpu-gpu-average :1-462&!.H=
crdaction cpu-gpu-trajectories matrix covar \
name cpu-gpu-covar :1-462&!.H=
runanalysis diagmatrix cpu-gpu-covar out cpu-gpu-evecs.dat \
vecs 3 name myEvecs \
nmwiz nmwizvecs 3 nmwizfile dna.nmd nmwizmask :1-462&!.H=
crdaction cpu-gpu-trajectories projection CPU modes myEvecs \
beg 1 end 3 :1-462&!.H= crdframes 1,200
hist CPU:1 bins 100 out cpu-gpu-hist.agr norm name CPU-1
hist CPU:2 bins 100 out cpu-gpu-hist.agr norm name CPU-2
hist CPU:3 bins 100 out cpu-gpu-hist.agr norm name CPU-3
run
clear all
readdata cpu-gpu-evecs.dat name Evecs
parm /projects/chem/ionic/abhi/CYP1/3pmo_CYP1-B/A_114/NEW_analysis/pca/3pm0_114.prmtop
parmstrip !(:1-462&!.H=)
parmwrite out cpu-gpu-modes.prmtop
runanalysis modes name Evecs trajout cpu-gpu-mode1.nc \
pcmin -100 pcmax 100 tmode 1 trajoutmask :1-462&!.H= trajoutfmt netcdf
Thanking you,
-Abhishek
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Received on Thu Jul 13 2017 - 20:30:02 PDT
