özge kül wrote:
Hi
Thank you for your advices.I want to ask a question.Is there a
difference in the MD simulation between A protein complex which has 2
chains and a molecule that has 1 chain?
Yes. There is difference. But somehow, you need to rephrase your question.
Are the parameters must be different ?Also I want to ask about
trajconv.Where I had to add the pbc?
the second step, editconf impose PBC onto the system.
I want to send you my directions.
1. pdb2gmx_mpi -f 1ppbfree.pdb -p 1ppbfree.top -o 1ppbfree.gro
2.editconf_mpi -f 1ppbfree.gro -o -d 0.8 -bt octahedron
3. genbox_mpi -cp out.gro -cs -p 1ppbfree.top -o 1ppbfree-gen.gro
4. grompp_mpi -v -f 1ppbfree-en.mdp -c 1ppbfree-gen.gro -o
1ppbfree-en.tpr -p 1ppbfree.top
5.mdrun_mpi -v -s 1ppbfree-en.tpr -o 1ppbfree-en.trr -c
1ppbfree-aftermin.gro -g 1ppbfree-en.log -e 1ppbfree-en.edr
or is the pbc used in the script?
Thank You very much....
Özge
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