[gmx-users] a question in energy minimization step

Banafsheh Mehrazma bmehrazma at gmail.com
Wed Jan 25 11:45:00 CET 2012

Hi everyone;
I am about to minimize a system in 3 steps;
first, I want my molecule to be minimized, so I used ''define =
-DPOSRES_WATER " in my *.mdp file., Then after using g_energy command to
make potential.xvg, it gave me a nice diagram. Next I wanted to perform
minimization with my protein to be constained and then a
whole_system_minimization without any constraints. However, the next
diagrams are not appropriate; one is linear, and another is increasing,
instead of decreasing!
I should mention that they all converged before 1340, 201, 47 steps,
respectively, and I set emtol option to be 100 and nsteps = 500000.
Do you know what is the problem?

yours sincerely
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