[gmx-users] Squishing or Stretching Membranes
tsjerkw at gmail.com
Wed Jul 10 11:21:48 CEST 2013
You can use editconf -scale to scale the system to the average box size.
On Jul 9, 2013 4:28 PM, "Mirco Wahab" <mirco.wahab at chemie.tu-freiberg.de>
On 09.07.2013 16:11, Neha wrote: > > I had a question about trjconv. After
one of my simulations has...
You could dump many structures from the last part of the trajectory, and:
- take one structure that has all box vectors almost at, but *below*
your target size,
- edit the bottom line of the coordinate file to the desired size,
- run some steps steepest descent minimization in order to correct
for some overstretched bonds of molecules crossing the PBC,
The absolute last configuration of your run has no "specific meaning"
in a statistical sense. You can use any other configuration from
the equilibrium-part of the run.
my € 0.02
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