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

[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 minim.mdp -c 5.gro -p topol.top
> 
> mdrun -s topol.tpr
> 
> grompp -f nvt.mdp -c confout.gro -p topol.top -o md.tpr
> 
> mdrun -s md.tpr
> 
> Whether the simulation is correct ?
> 

Is there some reason you think it isn't?

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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