[gmx-users] two chains

Yang Ye leafyoung81-group at yahoo.com
Fri Mar 30 04:08:09 CEST 2007

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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