[gmx-users] Squishing or Stretching Membranes

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Jul 10 11:21:48 CEST 2013

Hey :)

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,
 - run

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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