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Problem with polarizable water
- gbalogh
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8 years 7 months ago #4891
by gbalogh
Problem with polarizable water was created by gbalogh
Hello.
I was trying to solvate a protein with polarizable water using GROMACS. The energy minimalization finished, but there were some LINCS warnings (bonds rotated more than 30 degrees) at the beginning. The equilibration of the system terminated because of too many LINCS warinings (bonds in water molecules rotated too much).
I have also generated an empty water box using genbox. The energy minimization finished without problems after replacing constraints with bonds with large force constant, but mdrun crashed (segmentation fault) after about 100 steps during equilibration and printed lots of LINCS warnings (bonds in water molecules rotated too much).
In a previous forum topic it was suggested that one should generate a box of "normal" water and convert it to polarizable water, but I don't know exactly what it means. How can I calculate the coordinates of the WP and WM pseudo-atoms in each molecule?
Thanks in advance.
I was trying to solvate a protein with polarizable water using GROMACS. The energy minimalization finished, but there were some LINCS warnings (bonds rotated more than 30 degrees) at the beginning. The equilibration of the system terminated because of too many LINCS warinings (bonds in water molecules rotated too much).
I have also generated an empty water box using genbox. The energy minimization finished without problems after replacing constraints with bonds with large force constant, but mdrun crashed (segmentation fault) after about 100 steps during equilibration and printed lots of LINCS warnings (bonds in water molecules rotated too much).
In a previous forum topic it was suggested that one should generate a box of "normal" water and convert it to polarizable water, but I don't know exactly what it means. How can I calculate the coordinates of the WP and WM pseudo-atoms in each molecule?
Thanks in advance.
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- P_Banerjee
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8 years 6 months ago #4941
by P_Banerjee
Replied by P_Banerjee on topic Problem with polarizable water
Hey!,
Did you add solvent with the option -vdwd 0.21 to the genbox command? Also, use the .mdp parameters provided for the polarizable water model on the website. I could eqiulibrate my system with the same parameters.
Best,
Pallavi Banerjeee.
Did you add solvent with the option -vdwd 0.21 to the genbox command? Also, use the .mdp parameters provided for the polarizable water model on the website. I could eqiulibrate my system with the same parameters.
Best,
Pallavi Banerjeee.
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- mnmelo
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8 years 6 months ago #4988
by mnmelo
Replied by mnmelo on topic Problem with polarizable water
Thanks for contributing, Pallavi!
One other important change that will greatly improve your minimizations is to treat the polarizable water constraints as stiff bonds instead (but for minimization only!). The martini .itp file where the polarizable water is defined already has those changes in place, you just have to uncomment them.
See the more detailed explanation of this I gave in another post .
Good luck and let us know if it works.
Manel
One other important change that will greatly improve your minimizations is to treat the polarizable water constraints as stiff bonds instead (but for minimization only!). The martini .itp file where the polarizable water is defined already has those changes in place, you just have to uncomment them.
See the more detailed explanation of this I gave in another post .
Good luck and let us know if it works.
Manel
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- gbalogh
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8 years 6 months ago - 8 years 6 months ago #5002
by gbalogh
Replied by gbalogh on topic Problem with polarizable water
I have solvated the same system with "normal" water, converted water molecules to polarizable ones, and added ions. During energy minimization (with constraints in water molecules replaced with bonds), after about 140 steps the force started increasing heavily (>2e13 in the units of GROMACS) and the simulation stopped. (Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 200)
I have also noticed that the number of water molecules added is about 30% less when the system is solvated using polarizable water ( md.chem.rug.nl/images/applications/water/polarize-water.gro ). The size of the box and the "non-water" atoms are the same in both cases (vdwd=0.21).
requested precision Fmax < 200)
I have also noticed that the number of water molecules added is about 30% less when the system is solvated using polarizable water ( md.chem.rug.nl/images/applications/water/polarize-water.gro ). The size of the box and the "non-water" atoms are the same in both cases (vdwd=0.21).
Last edit: 8 years 6 months ago by gbalogh.
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