Re: [gmx-users] calculate potential in the box contain ions

2011-07-30 Thread Justin A. Lemkul
Please keep the discussion on the list; I'm not a private tutor. Saeid Akbarshahi wrote: Dear Justin I have simulated this system with this structure and files.Could you tell me, is my structure correct? I have no clue what is in your system, what settings were used for the simulation, o

Re: [gmx-users] calculate potential in the box contain ions

2011-07-30 Thread Justin A. Lemkul
Saeid Akbarshahi wrote: Deer users The simulation box contains sodium and chloride ions start simulation pdb2gmx -f ion.pdb -posrefc 0 Force Field : AMBER99SB-ILDN - Water TIP3P editconf -f conf.gro -bt cubic -box 3 3 3 genbox -cp out.gro -cs spc216.gro -o 5.gro -p topol.top grompp -f

[gmx-users] calculate potential in the box contain ions

2011-07-30 Thread Saeid Akbarshahi
Dear users The simulation box contains sodium and chloride ions start simulation pdb2gmx -f ion.pdb -posrefc 0 Force Field : AMBER99SB-ILDN  - Water TIP3P editconf -f conf.gro -bt cubic -box 3 3 3 genbox -cp out.gro -cs spc216.gro -o 5.gro -p topol.top grompp -f minim.mdp -c 5.gro -p topol

[gmx-users] calculate potential in the box contain ions

2011-07-30 Thread Saeid Akbarshahi
Deer users The simulation box contains sodium and chloride ions start simulation pdb2gmx -f ion.pdb -posrefc 0 Force Field : AMBER99SB-ILDN  - Water TIP3P editconf -f conf.gro -bt cubic -box 3 3 3 genbox -cp out.gro -cs spc216.gro -o 5.gro -p topol.top grompp -f minim.mdp -c 5.gro -p topo