[gmx-users] What is the best protocol for running a MD simulation using gromacs?

S. Alireza Bagherzadeh s.a.bagherzadeh.h at gmail.com
Sun Feb 3 01:03:11 CET 2013

Dear gmx-users,

As far as I understand, gromacs is mostly used for simulating biological
systems and in particular the proteins.

In my system, I am trying to simulate the decomposition of a solid
substance which
is very similar to ice. I take the initial configuration of this substance from
the single crystal x-ray diffraction experiment and I make my desired super
cell by replicating the unit cell in 3 dimensions.

Then, I would add liquid water to the sides of my super cell (along the
z-direction) using "genbox" utility.

I start my run by equilibrating the liquid waters, especially those at the
interface, in an NVT ensemble and afterwards I start my production NVE
run.I should also add that I keep my solid phase frozen during NVT and
unfreeze it during the NVE.

Would you please advise me if there is any better procedure to follow which
suits gromacs and my system the best?

S. Alireza Bagherzadeh
 PhD Candidate
Dept. of Chem. & Bio. Eng.
University of BC
2360 East Mall
Vancouver BC V6T1Z3

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