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Gro Macs

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4 views6 pages

Gro Macs

Uploaded by

vibhamishra017
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Running Gromacs

http://www.gromacs.org/

Input files: *.pdb, *.gro, *.itp, *.top, *.mdp, *.tpr

Output files: *.trr, *.xtc, *.edr, *.log

Input:

• pdb : Protein data bank format


• gro: Gromacs format (atom co-ordinates)
• itp: atom topologies (charges, mass, radii, etc)
• top: forcefields, number of molecules, water, etc
• mdp: molecular dynamics simulation parameters
• tpr: all of the above

Output:

• trr: trajectory file (co-ordinates and velocity)


• xtc: trajectory file (co-ordinates only)
• edr: trajectory file (energies)
• log: CPU time, MFLOP, etc.
Creating Input Files

Converting pdb to gro:

pdb2gmx –f input.pdb –o output.gro -o protein.top –inter


inter = interactive, (prompts you for different things
such as charge on polarizable residues,
protonoation state of histidine,
force-field
N-term, C-term patches (NH2, NH3, COO-, COOH)
Move protein.top to protein.itp

Solvation of the system:


editconf –f output.gro -box lx ly lz –o presol.gro

To check box size is OK


editconf –f presol.gro –o presol.pdb
Rasmol presol.pdb (graphics software)
Set unitcell on (check that protein is in the center of the
box and the edge is about 3 nm away from the protein)
Solvation (continued)

Once you are satisfied with the box


•Genbox –cp presol.gro –cs spc216.gro –o sol.gro
Spc216: spc water molecules (you can take any other
water type as well, tip3p, tip4p, tip5p)

Check once again that water and protein are inside the
box and check the box size
• Editconf –f sol.gro –o sol.pdb
• Rasmol sol.pdb
Set unitcell on

Electroneutrality:

If you are happy with the system, check the total charge. If
net charge is not zero, then add counter ions to get neutral
system. (select random water molecules and replace with
ion). Eg: H2O -> Cl- (remove H1, H2, and rename O as Cl-)
or use genion (which does the same thing)

Once again check the system with rasmol or any other


graphics software you like.
Creating tpr file

Grompp –f emin.mdp –p protein.top –c sol.gro -o emin.tpr

Protein.top: file which contains the following


protein.itp (created by pdb2gmx)
spc.itp
number of protein molecules
number of water molecules
number of counter ions

emin.mdp: molecular dynamics parameter file for energy


minimzation of the system. Energy minimization is a must,
before the production run.
To begin with, use the default parameters.

For all the gromacs commands, typing –h(help) will give


the various options available for each command:
Eg:
pdb2gmx- -h
Editconf –h
Genbox –h, (etc)
Running Gromacs

On the liszt server:


Groit –q –np –n –r –s
• q : que type (tenday, fourweek)
• np: number of processors (1 for energy
minimization)
• n: notify when job exits
• r : run (???)
• s: the tpr file (emin.tpr)

This will create the following outputs


emin.gro (energy minimized system in gro format)

emin.trr & emin.xtc : Co-ordinates and velocity (which


are not meaningful here)

emin.log: The log file which gives the final energy of the
system. Check to see that the energy is negative
Once you are satisfied with the energy minimzation,
Create the tpr file for the the MD simulation (production
run)

Grompp -np 2 –f md.mdp –p protein.top –c emin.gro -o md.tpr

Here you have to specify the number of processors, since


you can run it in parallel
np = 1 (two processors, 1 node on a dual node CPU)
2 (four processors, 2 nodes)

Run as: Groit –q –np –n –r –s

Do trajectory analysis using the gromacs software (check


gromacs online)
http://www.gromacs.org/documentation/reference_3.2/online.html

This link also gives example mdp files and the meaning of
each parameter.

Good Luck with your MD simulations!!

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