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计算G_mmpbsa

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#!/bin/bash
# author:kangsgo
# method:
# loop 后面为文件夹变量,表示进入哪个文件夹
# trj_125-150ns.xtc 轨迹变量
for loop in achmd bnf318 qna tcdd
do
echo "开始执行!";
echo "进入第一个目录:$loop!";
cd /home/gromacs/shiyan/$loop
echo "进行一步计算"
echo -e "1\n13\n"|g_mmpbsa -f trj_125-150ns.xtc -s npt.tpr -n index.ndx -i canshu/pbsa.mdp -pdie 2 -pbsa -decomp
echo "开始能量拆分"
python3 MmPbSaStat.py -m energy_MM.xvg -p polar.xvg -a apolar.xvg
python3 MmPbSaDecomp.py -bs -nbs 2000 -m contrib_MM.dat -p contrib_pol.dat -a contrib_apol.dat
echo "完成"
done

 

计算rmsf,并且处理轨迹

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#!/bin/bash
# author:kangsgo
# name: rmsf处理脚本
# method:
# loop 后面为文件夹变量,表示进入哪个文件夹
# trj_120-150ns.xtc 轨迹变量

for loop in bnf bnf318 ch qna tcdd
do
echo "开始执行";
echo "进入第一个目录$loop";
cd /home/kangsgo/shiyan/chuli/$loop
echo "转换轨迹";
trjconv_mpi -f mdwholeNOjump.xtc -o trj_120-150ns -b 120000 -e 150000
echo "转换完成,开始转换500个单位轨迹";
trjconv_mpi -f mdwholeNOjump.xtc -o md200skip -dt 200
echo "转换完成,开始转换100个单位轨迹";
trjconv_mpi -f mdwholeNOjump.xtc -o md1000skip -dt 1000
echo "rmsf计算"
echo -e "3\n"|gmx_mpi rmsf -s md_0_1.tpr -f trj_120-150ns.xtc -o rmsf.xvg -oq rmsf.pdb -res
done

echo "全部完成"

 

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