normal problems with water

  • irewood
  • irewood's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
9 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?

Please Log in or Create an account to join the conversation.

More
9 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)?

Please Log in or Create an account to join the conversation.

  • irewood
  • irewood's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
9 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)

Please Log in or Create an account to join the conversation.

More
9 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...

Please Log in or Create an account to join the conversation.

  • irewood
  • irewood's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
9 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"

Please Log in or Create an account to join the conversation.

More
9 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.

Please Log in or Create an account to join the conversation.

Time to create page: 0.087 seconds