I am trying to simulate a protein-ligand complex using Gromacs. I am currently working on CDK2/CDK4. I am following the tutorial for dynamics mentioned in the website http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/
I am supposed to simulate the complex at 1000 ps. The protocol worked fine for CDK4-ligand complexes, but it is not working for CDK2. After the Energy Minimization command, the em.gro file generated is very large approx 86 mb.(For CDK4-ligand complex the file generated was ~7 mb and other project students also generated a file less than 10 mb for their work) If the em is done with 100 steps it gives me LINCS warning so I did it with 500 steps. With this huge gro file, the NVT and NPT is generating rougly 40 gb of data collectively and taking a long time to complete.
Please help me.
I have also tried pdb2gmx -missing -f CDK2.pdb -o CDK2.gro command. Still not working for me. The commands are
pdb2gmx -f CDK2.pdb -o CDK2.gro -water spc
editconf -f conf.gro -o newbox.gro -bt dodecahedron -d 1.0
genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -np 4
grompp -f em_real.mdp -c solv_ions.gro -p topol.top -o em.tpr
mdrun -v -deffnm em
After this step em.gro file is generated.