[gmx-users] Lipid water simulation

Sheikh Imamul Hossain s.imamul.ku at gmail.com
Mon Mar 27 03:56:42 CEST 2017

Hi all,

I am trying to simulate 1024 dppc lipids with water. I have prepared my
system using Charmm-Gui monolayer builder. Then I converted the atomistic
system to coarse grained system using bacdward.py. The box size I got in
the gro file was 18.246   18.38  23.7. Then I added CG water between the
two dppc monolayers within the box 18.246   18.38    4.22. The I increased
the box size to 18.246  18.38    50.00. The total number of CG water is
6144. I minimized the system then equilibrated the system three times with
time steps 2fs, 10fs and 15fs. Then I did the production run for 2
microsecond using 20fs time steps. The temperature 310K was used in surface
tension coupling with surface tension 20mN/m per leaflet. I  have few

1. After the first equilibration some (very few) CG water found in the air
space of the box  i.e in the top and bottom of the dppc monolayers. Which
are supposed to be attached together with other water between the two
monolayer. Is there any solution to prevent this?

2. Is there any other option to build the CG monolayer system and adding CG
water between the two monolayers? I used gmx solvate to add water.

3. I used 6 CG water per lipid. How many CG water can be added against the
number of lipids?


After analyzing my system with the help of Bevan Lab DPPC tutorials I got
the area per lipid 0.5845. I used the formula
Area per lipid = (Box-X*Box-Y)/ # of lipid per leaflet

Thanks in advance.

Sincerely Your’s
Sheikh Imamul Hossain
PhD student at QUT

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