[gmx-users] Setting up a random system

erwin berthier erwindownunder at gmail.com
Sun Jul 9 15:11:17 CEST 2006

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).


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