? 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
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
