3.10 host guest 2

# 4090 /home/data/zzy/koff/smd/host-guest/test1
cp /home/data/zjhan/diffusion_calculation/aspirin/box_50/npt/npt.gro ./
cp /home/data/zjhan/diffusion_calculation/aspirin/box_50/gmx.top ./
cp /home/data/zjhan/diffusion_calculation/mdp/md.mdp ./


# mdp后添加以下字段：
# pull-group1-pbcatom 随便选的，因为asprin是个环
pull                    = yes
pull-group1-pbcatom     = 21
pull-pbc-ref-prev-step-com = yes
pull_ncoords            = 1         ; only one reaction coordinate
pull_ngroups            = 2         ; two groups defining one reaction coordinate
pull_group1_name        = MOL
pull_group2_name        = LIG
pull_coord1_type        = umbrella  ; harmonic potential
pull_coord1_geometry    = distance  ; simple distance increase
pull_coord1_dim         = Y Y Y
pull_coord1_groups      = 1 2
pull_coord1_start       = yes       ; define initial COM distance > 0
pull_coord1_rate        = 0.0001      ; 0.005 nm per ps = 10 nm per ns
pull_coord1_k           = 1000      ; kJ mol^-1 nm^-2

4090 /home/data/zzy/koff/smd/host-guest/
dddc@gpu-4090:/home/data/zzy/koff/smd/host-guest/test2$ nohup bash do.sh &
[1] 2293829

85.9 /home/databank/zzy/project/smd/host-guest/test1
(base) [chpeng@localhost test1]$ nohup bash do.sh &
[1] 56097

输入数据

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 $i;cp ../../$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}.txt;wc -l ../exp${i}.txt;done

# 85.9 /home/databank/zzy/project/smd/host-guest/test1/jarzynski-pmf/10smd-v_0.001
for i in {1..10};do sort -k4 -rg exp${i}.txt|head -n 2;done