Hello, I'm very sorry for the way I reply, the truth is that i didn't know how else to reply (it is my first time posting here).
the script to generate the REMD is: #!/bin/bash # ff opsla and water spc # echo -e "14\n4\n3\n3 0" |pdb2gmx -f 1.pdb -o inib4em.pdb -p topol.top -ignh -ter editconf -f inib4em.pdb -o inib4em.pdb -d 0.34 -bt dodecahedron grompp -v -f iniem.mdp -o em -c inib4em.pdb -maxwarn 5 mdrun -v -s em -c ini_after_em.pdb -deffnm ini_after_em editconf -f ini_after_em.pdb -o ini_after_em.pdb -d 0.34 -bt dodecahedron genbox -cp ini_after_em.pdb -cs spc216 -o sol_b4em.pdb -p topol.top grompp -v -f em.mdp -c sol_b4em.pdb -o sol_em -p topol.top -maxwarn 5 mdrun -v -s sol_em -c sol_after_em.pdb -deffnm sol_after_em grompp -v -f rp.mdp -c sol_after_em.pdb -o sol_rp -p topol.top -maxwarn 5 mdrun -v -s sol_rp -c sol_after_rp.pdb -deffnm sol_after_rp # NVT and NPT runs for each replica for ((i = 0; i<= 42 ; i ++)) do grompp -v -f nvt$i.mdp -c sol_after_rp.pdb -o sol_nvt$i -p topol.top -maxwarn 5 mdrun -v -s sol_nvt$i.tpr -c sol_after_nvt$i.pdb -deffnm sol_after_nvt$i grompp -v -f npt$i.mdp -c sol_after_nvt$i.pdb -o sol_npt$i -p topol.top -maxwarn 5 mdrun -v -s sol_npt$i.tpr -c sol_after_npt$i.pdb -deffnm sol_after_npt$i editconf -f sol_after_npt$i.pdb -o sol_after_nptt$i.pdb -c grompp -v -f solv$i.mdp -c sol_after_nptt$i.pdb -o sol_solv$i -p topol.top -maxwarn 5 done # REMD run mpiexec -l -np 43 mdrun_mpi -v -s sol_solv.tpr -multi 43 -replex 500 -c Folded.pdb -deffnm Folded Best regards
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