[gmx-users] Error while performing a REMD simulation

Luis Miguel Medina Solano migu-med at uniandes.edu.co
Sun Apr 10 03:19:14 CEST 2011


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:

# 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 ++))
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
# 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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