Re: [gmx-users] a fatal error in step mdrun -v -deffnm em

2016-03-30 Thread Justin Lemkul
On 3/30/16 8:36 AM, Brett wrote: Dear All, After steps for pdb2gmx, editconf, solvate, "-f ions.mdp -c target_solv.gro -p topol.top -o ions.tpr", genion, "grompp -f minim.mdp -c target_solv_ions.gro -p topol.top -o em.tpr", I started step "mdrun -v -deffnm em &", but in the "mdrun -v

Re: [gmx-users] a fatal error in step mdrun -v -deffnm em

2016-03-30 Thread Brett
gmx genion -s ions.tpr -o target_solv_ions.gro -p topol.top -pname NA -nname CL -neutral -conc 0.15 At 2016-03-30 21:38:49, "SAKO MIRZAIE" wrote: >let me see your neutralizing command to produce ions.tpr. > >On 3/30/16, Brett wrote: >> Dear

Re: [gmx-users] a fatal error in step mdrun -v -deffnm em

2016-03-30 Thread SAKO MIRZAIE
let me see your neutralizing command to produce ions.tpr. On 3/30/16, Brett wrote: > Dear All, > > After steps for pdb2gmx, editconf, solvate, "-f ions.mdp -c target_solv.gro > -p topol.top -o ions.tpr", genion, "grompp -f minim.mdp -c > target_solv_ions.gro -p topol.top -o

[gmx-users] a fatal error in step mdrun -v -deffnm em

2016-03-30 Thread Brett
Dear All, After steps for pdb2gmx, editconf, solvate, "-f ions.mdp -c target_solv.gro -p topol.top -o ions.tpr", genion, "grompp -f minim.mdp -c target_solv_ions.gro -p topol.top -o em.tpr", I started step "mdrun -v -deffnm em &", but in the "mdrun -v -deffnm em &" step it gave "Step= 15,

[gmx-users] a fatal error in step mdrun -v -deffnm em

2016-03-30 Thread Brett
Dear All, After steps for pdb2gmx, editconf, solvate, "-f ions.mdp -c target_solv.gro -p topol.top -o ions.tpr", genion, "grompp -f minim.mdp -c target_solv_ions.gro -p topol.top -o em.tpr", I started step "mdrun -v -deffnm em &", but in the "mdrun -v -deffnm em &" step it gave "Step= 15,