hnishi

/*
USAGE: ./09cent 03_V2.log str2 str3
str2: RESIDUE NUMBER ( "105" "114" etc )
str3: COEFFICIENT OF SIGMA ( "2" "0" etc )
	Especially "0" is selected as a coefficient, then all data of group are putout
INPUT: ./pdbtmp/...
OUTPUT: ./result/...
*/
#include<stdio.h>
#include<string.h>

hnishi

#!/bin/sh

cmake /home/jykang/hnishi/gromacs-4.6.6  \
         -DGMX_BUILD_OWN_FFTW=on \
         -DCMAKE_INSTALL_PREFIX=/home/jykang/hnishi/programs/gromacs-4.6.6_serial \
         -DGMX_DOUBLE=ON \
         -DBUILD_SHARED_LIBS=off \
         -DCMAKE_C_COMPILER=/opt/intel/composer_xe_2011_sp1.6.233/bin/intel64/icc \
         -DCMAKE_CXX_COMPILER=/opt/intel/composer_xe_2011_sp1.6.233/bin/intel64/icc \
         -DGMX_FFT_LIBRARY=mkl  \

hnishi

function ncalc(){
  command echo "$1" | bc -l | sed -e 's/^\./0\./' -e 's/-\./-0\./'
}

# source ncalc.bash  or  copy into ~/.bashrc
# and you can use ncalc command
# ncalc 60*2/3

hnishi

trjconv_mpi_d -f npt.trr -s ../00_add_cl/form3.pdb -o traj_out.pdb

hnishi

title               =  main_MD 
define              =  -DPOSRES_MG ; position restraint

integrator          =  md   ; md: leap-frog
tinit               =  0.0   ; 
dt                  =  0.002   ; ps
nsteps              =  10000000     ; maximum step (ps), -1 means no limit

comm-mode           =  Linear  ; com, Linear: translation, Angular: trans. and rotation, None
nstcomm             =  5   ;frequency for com motion removal

hnishi

ls |grep -v trr|xargs -I{} cp -r {} ../51_norest/

hnishi

set terminal png
#set terminal postscript eps color enhanced
#set terminal pdf	# not work
set nokey

set xlabel "Potential energy (kcal/mol)"

set ylabel "ln(P)" 
set yrange [-20:0]
#set xrange [110:130]

hnishi

#set term pngcairo transparent
#set output "trjpc.png"

set term svg enhanced font "Arial, 12" # in svg, 100=1inch
set output "output.svg"
set encoding iso_8859_1

#set title "Free energy landscape"
#set nokey
set grid

hnishi

import sys
import numpy as np

f = open('whole.fort.12', 'r')

rgas = 8.31451/4.184/1000

energy = []
lnnE = []

hnishi

# prjnishi.py v 1.0
# projection into PC space with a PCA eigenvector and average.
import sys
import numpy as np
from optparse import OptionParser

############ argument ##############
parser = OptionParser

def get_options():