[gmx-users] Squishing or Stretching Membranes
mirco.wahab at chemie.tu-freiberg.de
Tue Jul 9 16:27:43 CEST 2013
On 09.07.2013 16:11, Neha wrote:
> I had a question about trjconv. After one of my simulations has ended I want
> to use the final structure file to run some other simulations. However, what
> I want to do is run an NVT run using the average box size of the earlier
> run. Since the final structure file will most likely not be at the exact
> average I was wondering if I could use trjconv -pbc mol to put all the atoms
> in a box either smaller or bigger than the original.
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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