2.26 smd+jazynsiki

数据整理

# 85.9 /home/databank/zzy/project/smd/hiv-1/smd2/analysis/from-git/ala10/
# 对git上的一个程序进行修改 EricBoittier/ala10 at f9112280820f10e2942d113a9933471c786ed9a7
# /home/databank/zzy/project/smd/hiv-1/smd2/analysis/from-git/ala10/Practical.ipynb
# 将 smd_pullf.xvg 与 smd_pullx.xvg 整理成 da_smd_tcl.out 的 格式


# /home/databank/zzy/project/smd/hiv-1/smd2/analysis/A016/1smd-v_0.05
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 !=""' > /home/databank/zzy/project/smd/hiv-1/smd2/analysis/zzy-test1/gmx-single-smd-result.txt


# /home/databank/zzy/project/smd/hiv-1/smd2/analysis/zzy-test1/5repeat
sed '/^#/d' 1/smd_pullx.xvg|sed '/^@/d' |awk '{print $1}' >timestep
for i in {1..5};do sed '/^#/d' $i/smd_pullx.xvg|sed '/^@/d' |awk '{print $2}' >distance${i};done
for i in {1..5};do sed '/^#/d' $i/smd_pullf.xvg|sed '/^@/d' |awk '{print $2}' >force${i};done
paste -d ' ' timestep distance1 distance2 distance3 distance4 distance5 force1 force2 force3 force4 force5|awk '$11 !=""'  > ../gmx-5repeat-smd-result.txt


# /home/databank/zzy/project/smd/hiv-1/smd2/analysis/A016/slow-smd-test
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 !=""' > /home/databank/zzy/project/smd/hiv-1/smd2/analysis/zzy-test1/gmx-slow-pull-distance.txt

PMF

# 现在还剩下慢速的smd模拟结果文件 Fexact.dat 没弄清楚它
# 2-27 22：19 初步判断他就是该体系在接近真实的条件下（pull speed很慢）得到的PMF
# 横坐标为反应坐标，从13埃米左右开始，纵坐标就是自由能变化情况

# 85.9 /home/databank/zzy/project/smd/hiv-1/smd2/analysis/A016/slow-smd-test
# 交了一个比原 pull speed 慢10倍的SMD模拟任务，模拟步数增加了100倍以避免配体不解离
# 2-27 已完成

1. 搞清楚PMF怎么计算的，从公式上理解
2. 
   

后续计划

1. 看能不能输出做功的数值