[gmx-users] two chains
Mark.Abraham at anu.edu.au
Fri Mar 30 02:57:01 CEST 2007
You've asked four different questions in the space of one paragraph,
with little clarity. Please consider asking each question with some
organised background information that you think will help us give you
the answer you want.
> 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?
No. If there's a covalent link then they'll need to end up as one
molecule, otherwise more than one.
> Are the parameters must be
> different ?
No. Why would they?
> Also I want to ask about trajconv.
What did you want to ask? :-)
> Where I had to add the
> pbc?I want to send you my directions.
As Dallas said, you introduce pbc with your choice of parameters in your
.mdp file. It sounds like you should learn some things by looking at
your .mdp files and understanding the effects of each parameter by
looking them up in section 7.3
> 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?
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