Re: [gmx-users] two chains

[Yang Ye]

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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Re: [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
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RE: [gmx-users] two chains

[Dallas B. Warren]

Ozge,

>4.  grompp_mpi -v -f 1ppbfree-en.mdp -c 1ppbfree-gen.gro -o
1ppbfree-en.tpr -p 1ppbfree.top

1ppbfree-en.mdp is the file in which the PBC is specified or not.  So
from that time on, when you run the simulation, what ever you set in
terms of the PBC within that file are applied.

Catch ya,

Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
[EMAIL PROTECTED]
+61 3 9903 9524
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.
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[gmx-users] two chains

[�zge]

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?Are the parameters must be different ?Also I want to ask about 
trajconv.Where I had to add the pbc?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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