[gmx-users] two chains

[Mark Abraham]

? wrote:
> Hi
>  

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?

What script?

Mark