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
--
========================================
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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