- Posts: 19
Water file
- xudongh
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11 years 5 months ago - 11 years 5 months ago #1259
by xudongh
Water file was created by xudongh
Hello all,
www.bevanlab.biochem.vt.edu/Pages/Person...zyme/01_pdb2gmx.html
When attempting to follow other tutorials such as Lysozyme In water except I CG the lysozyme 1AKI and running the tutorial with a coase grained system. But in the steps of solvating the system with water with genbox, it calls for spc216.gro, but I realized that it loads my box with atom modeled water molecule, but my goal is to get it all in coase grain.
Where can I obtain CG modeled Water, or better, how would I go about to make a CG water model and run minimization on it? Because i noticed with the current martinize.py script, whenever you run it, it removes all the water molecules from your .PDB file.
Let me know!
P.S the reason i ask about this is because when I solvate with the water-1bar-303K.gro, and perform energy minimization run on the solvated system, the system stops after 14step of run, and claim it converged in less than 14 steps, but did not converge to Fmax . And according to the Lysozyme in water tutorial ( www.bevanlab.biochem.vt.edu/Pages/Person...zyme/01_pdb2gmx.html ) , the potential energy outcome from this energy minimization should definitely be NEGATIVE and in the order of 10e5 and 10e6,. Logically, since I am converting an AA to CG system, it should still produce close range similarities of outcome in all energy minimization? My result should not differ from the tutorial?
Thanks
www.bevanlab.biochem.vt.edu/Pages/Person...zyme/01_pdb2gmx.html
When attempting to follow other tutorials such as Lysozyme In water except I CG the lysozyme 1AKI and running the tutorial with a coase grained system. But in the steps of solvating the system with water with genbox, it calls for spc216.gro, but I realized that it loads my box with atom modeled water molecule, but my goal is to get it all in coase grain.
Where can I obtain CG modeled Water, or better, how would I go about to make a CG water model and run minimization on it? Because i noticed with the current martinize.py script, whenever you run it, it removes all the water molecules from your .PDB file.
Let me know!
P.S the reason i ask about this is because when I solvate with the water-1bar-303K.gro, and perform energy minimization run on the solvated system, the system stops after 14step of run, and claim it converged in less than 14 steps, but did not converge to Fmax . And according to the Lysozyme in water tutorial ( www.bevanlab.biochem.vt.edu/Pages/Person...zyme/01_pdb2gmx.html ) , the potential energy outcome from this energy minimization should definitely be NEGATIVE and in the order of 10e5 and 10e6,. Logically, since I am converting an AA to CG system, it should still produce close range similarities of outcome in all energy minimization? My result should not differ from the tutorial?
Thanks
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- richor
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11 years 5 months ago #1260
by richor
Replied by richor on topic Water file
Hello xudongh,
You can find the cg water here:
md.chem.rug.nl/cgmartini/index.php/downl...example-applications
At the "Pure water solvent" part.
You can find the cg water here:
md.chem.rug.nl/cgmartini/index.php/downl...example-applications
At the "Pure water solvent" part.
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- xudongh
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11 years 5 months ago #1262
by xudongh
Replied by xudongh on topic Water file
@ richor,
thank you very much!
thank you very much!
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