[gmx-users] Energy minimisation goes to several values

[Kevin C Chan]

Dear Users,

I am energy minimising a quite large solvated system containing protein and
lipids (~800,000 atoms). I used to fix components of the system in order to
speed-up energy minimisation and sometimes it is easier to debug such
processes. Here is my protocol:
1. fix all except water and so to minimise water
2. fix water and then minimise all the rest atoms
3. fix nothin and then minimise the whole system

While monitoring the energy of the system thought minimisations, it goes
fine for step 1 and 2 and converged after just few hundred steps. However
it goes back to several higher values of energy (bouncing between the
values) and they started to increase very slowly for step 3. This makes no
sense to me and did anyone have a similar experience?

There are two unusual points:
1. The system energy drops suddenly instead of decreased gradually during
step2 and then stays at a constant value.
2. If I use the resulting structure from step3 to proceed a, say, heating
process, it simply blows up.

To be clear, my system was solvated and auto-ionized using VMD tools and
some water inside the membrane has been directly deleted. Backbone of the
protein and phosphorus atoms of the membrane are under a
position constraint during all the minimisations. I was choosing conjugate
gradient for minimization.

Thanks in advance,
Kevin
City University of Hong Kong