demux

我们希望轨迹具有连续的坐标，尽管在系综空间中存在“跳跃”。这意味着将每个轨迹文件切成碎片，然后以正确的顺序粘贴回去。随Gromacs一起安装的Perl脚本demux.pl（在Gromacs安装目录下的bin目录下）将分析一个 .log文件，并写入两个特殊的.xvg文件，这些文件为转换矩阵，描述了轨迹时间序列从一个到另一个以及返回的过程。trjcat -demux可以使用这些文件为您对轨迹文件进行剪切和粘贴。

生成replica_index.xvg

pwd
/home/databank/zzy/project/trip13/analysis/0415/demux

locate gromacs-5.1.4/scripts/demux.pl 

perl /home/dddc/software/gromacs-5.1.4-vsremd/gromacs-5.1.4/scripts/demux.pl md0.log
-----------------------------------------------------------------
Going to read a file containing the exchange information from
your mdrun log file (md0.log).
This will produce a file (replica_index.xvg) suitable for
demultiplexing your trajectories using trjcat,
as well as a replica temperature file (replica_temp.xvg).
Each entry in the log file will be copied 0 times.
-----------------------------------------------------------------
There are 28 replicas.


Finished writing replica_index.xvg and replica_temp.xvg with 250000 lines

(base) [dddc@localhost demux]$ ls
md0.log  replica_index.xvg  replica_temp.xvg

各副本轨迹reconnected

(base) [dddc@localhost 1ns]$ gmx_mpi trjcat -f ../../../0415_500ns/vsremd20230609/500ns/cpp/04150.xtc ../../../0415_500ns/vsremd20230609/500ns/cpp/04151.xtc ../../../0415_500ns/vsremd20230609/500ns/cpp/04152.xtc ../../../0415_500ns/vsremd20230609/500ns/cpp/04153.xtc  ../../../0415_500ns/vsremd20230609/500ns/cpp/04154.xtc
../../../0415_500ns/vsremd20230609/500ns/cpp/04155.xtc
../../../0415_500ns/vsremd20230609/500ns/cpp/04155.xtc
../../../0415_500ns/vsremd20230609/500ns/cpp/04156.xtc
../../../0415_500ns/vsremd20230609/500ns/cpp/04157.xtc
../../../0415_500ns/vsremd20230609/500ns/cpp/04158.xtc
../../../0415_500ns/vsremd20230609/500ns/cpp/04159.xtc
../../../0415_500ns/vsremd20230609/500ns/cpp/041510.xtc 
../../../0415_500ns/vsremd20230609/500ns/cpp/041511.xtc 
../../../0415_500ns/vsremd20230609/500ns/cpp/041512.xtc 
../../../0415_500ns/vsremd20230609/500ns/cpp/041513.xtc 
../../../0415_500ns/vsremd20230609/500ns/cpp/041514.xtc 
../../../0415_500ns/vsremd20230609/500ns/cpp/041515.xtc 
../../../0415_500ns/vsremd20230609/500ns/cpp/041516.xtc 
../../../0415_500ns/vsremd20230609/500ns/cpp/041517.xtc 
../../../0415_500ns/vsremd20230609/500ns/cpp/041518.xtc
../../../0415_500ns/vsremd20230609/500ns/cpp/041519.xtc
../../../0415_500ns/vsremd20230609/500ns/cpp/041520.xtc
../../../0415_500ns/vsremd20230609/500ns/cpp/041521.xtc
../../../0415_500ns/vsremd20230609/500ns/cpp/041522.xtc
../../../0415_500ns/vsremd20230609/500ns/cpp/041523.xtc
../../../0415_500ns/vsremd20230609/500ns/cpp/041524.xtc
../../../0415_500ns/vsremd20230609/500ns/cpp/041525.xtc
../../../0415_500ns/vsremd20230609/500ns/cpp/041526.xtc
../../../0415_500ns/vsremd20230609/500ns/cpp/041527.xtc -demux replica_index.xvg 


(base) [dddc@localhost 1ns]$ ls
0_trajout.xtc  3_trajout.xtc  6_trajout.xtc
1_trajout.xtc  4_trajout.xtc  replica_index.xvg
2_trajout.xtc  5_trajout.xtc  replica_temp.xvg

周期性处理

gmx_mpi trjconv -f 0_trajout.xtc -s /home/dddc/lywu/koff/oame-g4/pre/funnel-vsremd/1ns/md0.tpr -pbc mol -ur compact -center -o 0_trajout_nopbc_nowater.xtc 

align 

gmx_mpi trjconv -f 6_trajout_nopbc_nowater.xtc -s /home/dddc/lywu/koff/oame-g4/pre/funnel-vsremd/1ns/md0.tpr -fit rot+trans -o look6.pdb

500ns轨迹处理

生成replica_index.xvg

(base) [dddc@localhost 500ns]$ perl /home/dddc/software/gromacs-5.1.4-vsremd/gromacs-5.1.4/scripts/demux.pl /home/dddc/lywu/koff/oame-g4/pre/funnel-vsremd/500ns/md0.log 
-----------------------------------------------------------------
Going to read a file containing the exchange information from
your mdrun log file (/home/dddc/lywu/koff/oame-g4/pre/funnel-vsremd/500ns/md0.log).
This will produce a file (replica_index.xvg) suitable for
demultiplexing your trajectories using trjcat,
as well as a replica temperature file (replica_temp.xvg).
Each entry in the log file will be copied 0 times.
-----------------------------------------------------------------
There are 7 replicas.
Finished writing replica_index.xvg and replica_temp.xvg with 249501 lines


(base) [dddc@localhost 500ns]$ ls
replica_index.xvg  replica_temp.xvg

各副本轨迹reconnected

(base) [dddc@localhost 500ns]$ cat reconnected.sh 
gmx_mpi trjcat -f /home/dddc/lywu/koff/oame-g4/pre/funnel-vsremd/500ns/md0.xtc /home/dddc/lywu/koff/oame-g4/pre/funnel-vsremd/500ns/md1.xtc /home/dddc/lywu/koff/oame-g4/pre/funnel-vsremd/500ns/md2.xtc /home/dddc/lywu/koff/oame-g4/pre/funnel-vsremd/500ns/md3.xtc /home/dddc/lywu/koff/oame-g4/pre/funnel-vsremd/500ns/md4.xtc /home/dddc/lywu/koff/oame-g4/pre/funnel-vsremd/500ns/md5.xtc /home/dddc/lywu/koff/oame-g4/pre/funnel-vsremd/500ns/md6.xtc -demux replica_index.xvg


(base) [dddc@localhost 500ns]$ nohup sh reconnected.sh &

周期性处理

whole

(base) [dddc@localhost pbc-test]$ echo 1|gmx_mpi trjconv  -f ../0_trajout.xtc -s /home/dddc/lywu/koff/oame-g4/pre/funnel-vsremd/1ns/md0.tpr -pbc whole -o 0_whole.xtc

nojump

(base) [dddc@localhost pbc-test]$ echo 1|gmx_mpi trjconv  -f 0_whole.xtc -s /home/dddc/lywu/koff/oame-g4/pre/funnel-vsremd/1ns/md0.tpr -pbc nojump -o 0_nojump.xtc

mol

(base) [dddc@localhost pbc-test]$ echo 3 1|gmx_mpi trjconv  -f 0_nojump.xtc -s /home/dddc/lywu/koff/oame-g4/pre/funnel-vsremd/1ns/md0.tpr -pbc mol -ur compact -center -o  0_mol.xtc

fit

(base) [dddc@localhost pbc-test]$ echo 0 0|gmx_mpi trjconv  -f 0_mol.xtc -s ../ref_nopbc_nowater.pdb -fit rot+trans -o  0_fit.xtc

计算RMSD