| MD simulations in the cluster | |||
| 작성일 | 2022-12-07 | 조회수 | 77 |
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| 첨부파일 | |||
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The README script has been modified for bash shell. Use the following file (gmx.sh). After creating the file, make it executable with the following command. chmod +x gmx.sh =========== gmx.sh ================= #!/usr/bin/env bash export PATH=/data/apps/cuda/cuda-11.6/bin:$PATH export LD_LIBRARY_PATH=/data/apps/cuda/cuda-11.6/lib64:$LD_LIBRARY_PATH source /data/apps/gromacs/2022.2/bin/GMXRC init=step3_input mini_prefix=step4.0_minimization equi_prefix=step4.1_equilibration prod_prefix=step5_production prod_step=step5 # Minimization # In the case that there is a problem during minimization using a single precision of GROMACS, please try to use # a double precision of GROMACS only for the minimization step. gmx grompp -f ${mini_prefix}.mdp -o ${mini_prefix}.tpr -c ${init}.gro -r ${init}.gro -p topol.top -n index.ndx -maxwarn -1 gmx mdrun -v -deffnm ${mini_prefix} -ntmpi 1 # Equilibration gmx grompp -f ${equi_prefix}.mdp -o ${equi_prefix}.tpr -c ${mini_prefix}.gro -r ${init}.gro -p topol.top -n index.ndx -maxwarn -1 gmx mdrun -deffnm ${equi_prefix} -ntmpi 1 # Production cnt=1 cntmax=10 while [ $cnt -le $cntmax ]; do ((pcnt=cnt-1)) istep=${prod_step}_${cnt} pstep=${prod_step}_${pcnt} if [ $cnt == 1 ]; then pstep=${equi_prefix} gmx grompp -f ${prod_prefix}.mdp -o ${istep}.tpr -c ${pstep}.gro -t ${pstep}.cpt -p topol.top -n index.ndx -maxwarn -1 gmx mdrun -deffnm ${istep} -ntmpi 1 else gmx convert-tpr -s ${pstep}.tpr -o ${istep}.tpr -extend 1000.0 gmx mdrun -s ${istep}.tpr -cpi ${pstep}.cpt -cpo ${istep}.cpt -deffnm ${prod_step}_1 -noappend -ntmpi 1 fi ((cnt++)) done ================================================== In addition, REMOVE the following two lines in the all ??.mdp files. nstvout = 5000 nstfout = 5000 THEN,
submit the job with the following command ./condor.sh 1qna
The files, condor.sh and gmx.sh are in the following directory. /data/myunggi/class/tutorial/protein/charmm-gui-6598610197/gromacs/ |
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| 다음 | Job submission on the computer cluster |
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| 이전 | Linux commands |