normal problems with water

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4 years 11 months ago #3679 by irewood
problems with water was created by irewood
Hi all,
I have simulated my systems (POPC bilayer and drug) with standard Martini CG water without any problem..
the, I have selected specifics .gro and convert W in PW with triple-w.py script, I had no problem.
But I'm trying to minimize/equilibrate the systems and the maximum ts without errors that I have reached is 0.001. Then I had lincs and systems crash (the bilayer is compressed and seems to has deformations).
I have found in the martini web, polarizable water section, that is possible to change constraints by bonds.
This is applied only at minimization step? for water or any part of the system??
I really do not understand what is happen and how I resolve it..
any clue?

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4 years 11 months ago #3680 by mnmelo
Replied by mnmelo on topic problems with water
Hi,

Did you change the dielectric constant to 2.5 for the polarizable water?
What about the minimization step after conversion of the waters, does it finish properly at low force values (in the 10^2 order)?

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4 years 11 months ago #3701 by irewood
Replied by irewood on topic problems with water
Hi,

Did you change the dielectric constant to 2.5 for the polarizable water? YES
What about the minimization step after conversion of the waters, does it finish properly at low force values (in the 10^2 order)? the obtained final forces were 4.5059977e+04 (max) and 7.6590277e+02 (norm)

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4 years 11 months ago #3702 by Clement
Replied by Clement on topic problems with water
You might need to increase the number of steps of minimization then...

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4 years 11 months ago #3703 by irewood
Replied by irewood on topic problems with water
When I minimize system gromacs returns: "Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision"

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4 years 11 months ago #3705 by Clement
Replied by Clement on topic problems with water
Then there's a problem with the system. Try with another snapshot, simulate the system with regular Martini for a few steps (couple nanoseconds), extract another frame and try again on that one.

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