[gmx-users] Setting up a random system

Mark Abraham mark.abraham at anu.edu.au
Sun Jul 9 15:32:36 CEST 2006

> Hello,
> I am trying to reproduce the assembly of phospholipids into a micel
> and so I fill a box using the genbox command. And then I solvate it
> using the same command.
> I have tried really hard to have it running but I get a segmentation
> fault at worst and at best a pressure scalling warning after a couple
> steps and then a segmentation fault.
> I use the -vdwd option so that the molecules aren't too close. If I
> fill the box by using the lipid as a solvant then I can get a box to
> work (although all the lipids are parallel to each other) but if I
> make the box twice as big it crashes once more... I should add that I
> manage to make it work fine with just the solvant, the problem occurs
> when I put long chains.
> Would there be a solution to limit artificially the velocities of the
> particles during the stabilization at the begining? Are there rules to
> follow when setting up a system? It seems that it is a problem that
> other people had but there is no clear methodology, I would be
> greatfull to have some general tips or links on how to start a random
> mix of solvant and lipids (or long molecules).

Have you minimised the energy to relieve bad contacts before starting MD?
Have you tried position-restrained MD to start the equilibration process?
Have you tried raising the temperature gradually rather than in one step?


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