normal water beads overlapping-incorrect surface tension values

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11 years 9 months ago #1047 by maruthi
Hi all,
I am trying to generate a small water box using water-1bar-303K.gro file using option genbox -cs water-1bar-303K.gro -box 10 10 10 -vdwd 0.21 -o water.gro, when i try to generate box some water beads are overlapping one over the other even though i maintain vdw radii. Please suggest me a way to avoid overlapping of beads on one over another.(for some xyz box sizes they are not overlapping)

2) After generating box (which does not contain overlapping beads) , i calculated surface tension value in gromacs for this water beads, by extending box in z axis, thus creating a surface.The value of surface tension which i got is too low 1.12 mN/m. Can you explain me why and where i went wrong.
Your advice is valuable,
Thanking you
Mohan

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11 years 9 months ago #1049 by djurre
1) We've seen that happen before. Possibly a bug/feature of genbox. Try using genconf.

2)The surface tension is to low compare to what? What kind of pressure coupling are you using? What is the ST in the x/y dimensions?

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11 years 9 months ago #1050 by maruthi
Hi,
Thanks for your reply, i will try to use genconf. The value of surface tension is not matching with experimental value of surface tension nor it is matching with the calculated surface tension for martini water that is 33mN/m. The simulations are performed in nvt conditions , there is no pressure coupling. I have not calculated surface tension in x/y direction since surface is formed in z direction. Please can you suggest me where i went wrong.

Thanking you,
Mohan

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