3.6 jarzynski PMF

85.9 /home/databank/zzy/project/smd/hiv-1/smd3/jarzynski-pmf/B439-test/jarzynski-PMF-test.ipynb

输入数据

单次SMD模拟测试

# 85.9 /home/databank/zzy/project/smd/hiv-1/smd3/jarzynski-pmf/test
cp ../../10_repeat_v_0.01/B439/1/*xvg ./
sed '/^#/d' smd_pullx.xvg|sed '/^@/d' |awk '{print $1}' >timestep
sed '/^#/d' smd_pullx.xvg|sed '/^@/d' |awk '{print $2}' >distance
sed '/^#/d' smd_pullf.xvg|sed '/^@/d' |awk '{print $2}' >force


# 组合三个数据，统一行数
# 删除牵引力为负值的行
# 确保distance单调递增
# 计算dx，删除第一行（dx为空）


paste -d ' ' timestep distance force|awk '$3 !=""'|awk 'NR==1 {print $0, "Diff"; prev=$2; next} {diff = $2 - prev; print $0, diff; prev=$2}'|sed '1d'|awk '$2 > 0{print}'|awk '$4 > 0{print}' >../test.txt


paste -d ' ' timestep distance force|awk '$3 !=""'|awk '$3 > 0{print}'|awk 'NR==1 { print; prev = $2; next } { if ($2 > prev) { print; prev = $2 } }'|awk 'NR==1 {print $0, "Diff"; prev=$2; next} {diff = $2 - prev; print $0, diff; prev=$2}'|sed '1d'>../test.txt

10次SMD（v=0.01nm/ps)

# 85.9 /home/databank/zzy/project/smd/hiv-1/smd3/jarzynski-pmf/10smd-v_0.01
for i in {1..10};do mkdir -p $i;cp ../../10_repeat_v_0.01/B439/$i/*xvg ./$i/;done


mkdir clean
cd clean
# 得到第一列 timestep 单位 ps
for i in {1..10};do sed '/^#/d' ../$i/smd_pullx.xvg|sed '/^@/d' |awk '{print $1}' >timestep${i};done
# 得到第2-11列 配体质心移动距离
for i in {1..10};do sed '/^#/d' ../$i/smd_pullx.xvg|sed '/^@/d' |awk '{print $2}' >distance${i};done
# 得到第12-21列 牵引力
for i in {1..10};do sed '/^#/d' ../$i/smd_pullf.xvg|sed '/^@/d' |awk '{print $2}' >force${i};done


for i in {1..10};do paste -d ' ' timestep${i} distance${i} force${i}|awk '$3 !=""'|awk '$3 > 0{print}'|awk 'NR==1 { print; prev = $2; next } { if ($2 > prev) { print; prev = $2 } }'|awk 'NR==1 {print $0, "Diff"; prev=$2; next} {diff = $2 - prev; print $0, diff; prev=$2}'|sed '1d'>../exp${i}_v-0.01.txt;wc -l ../exp${i}_v-0.01.txt;done

10次SMD（v=0.001nm/ps)

# 85.9 /home/databank/zzy/project/smd/hiv-1/smd3/jarzynski-pmf/10smd-v_0.001
for i in {1..10};do mkdir -p $i;cp ../../10_repeat_v_0.001/B439/$i/*xvg ./$i/;done


mkdir clean
cd clean
# 得到第一列 timestep 单位 ps
for i in {1..10};do sed '/^#/d' ../$i/smd_pullx.xvg|sed '/^@/d' |awk '{print $1}' >timestep${i};done
# 得到第2-11列 配体质心移动距离
for i in {1..10};do sed '/^#/d' ../$i/smd_pullx.xvg|sed '/^@/d' |awk '{print $2}' >distance${i};done
# 得到第12-21列 牵引力
for i in {1..10};do sed '/^#/d' ../$i/smd_pullf.xvg|sed '/^@/d' |awk '{print $2}' >force${i};done


for i in {1..10};do paste -d ' ' timestep${i} distance${i} force${i}|awk '$3 !=""'|awk '$3 > 0{print}'|awk 'NR==1 { print; prev = $2; next } { if ($2 > prev) { print; prev = $2 } }'|awk 'NR==1 {print $0, "Diff"; prev=$2; next} {diff = $2 - prev; print $0, diff; prev=$2}'|sed '1d'>../exp${i}_v-0.001.txt;wc -l ../exp${i}_v-0.001.txt;done

取平均