3.5 jarzynski PMF

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
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' > ../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


# 得到第一列 timestep 单位 ps
sed '/^#/d' 1/smd_pullx.xvg|sed '/^@/d' |awk '{print $1}' >timestep
# 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
# 得到第22-31列　计算dx即 固定时间间隔（dt） 内配体质心移动的距离
for i in {1..10};do awk 'NR>1 {print $1 - prev} {prev=$1}' distance${i}|sed '1i dx' >dx${i};done


paste -d ' ' timestep distance1 distance2 distance3 distance4 distance5 distance6 distance7 distance8 distance9 distance10 force1 force2 force3 force4 force5 force6 force7 force8 force9 force10 dx1 dx2 dx3 dx4 dx5 dx6 dx7 dx8 dx9 dx10|awk '$31!=""'|sed '1d'  > ../10smd-v_0.01.txt

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


# 得到第一列 timestep 单位 ps
sed '/^#/d' 1/smd_pullx.xvg|sed '/^@/d' |awk '{print $1}' >timestep
# 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
# 得到第22-31列　计算dx即 固定时间间隔（dt） 内配体质心移动的距离
for i in {1..10};do awk 'NR>1 {print $1 - prev} {prev=$1}' distance${i}|sed '1i dx' >dx${i};done


paste -d ' ' timestep distance1 distance2 distance3 distance4 distance5 distance6 distance7 distance8 distance9 distance10 force1 force2 force3 force4 force5 force6 force7 force8 force9 force10 dx1 dx2 dx3 dx4 dx5 dx6 dx7 dx8 dx9 dx10|awk '$31!=""'|sed '1d'  > ../10smd-v_0.001.txt

PMF

测试

10repeat v=0.01nm/ps

10repeat v=0.001nm/ps