From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Thu Jun 25 2015 - 11:32:10 CDT
I am energy minimising a quite large solvated system containing protein and
lipids. 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
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. I have tried switching on steep descent for step3 but it reports
some RATTLE errors which might indicate bad a structure after step2?
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.
Thanks in advance,
City University of Hong Kong
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