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

[S. Alireza Bagherzadeh]

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
I
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