[gmx-users] a question in energy minimization step

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jan 25 12:41:13 CET 2012

On 25/01/2012 9:45 PM, Banafsheh Mehrazma wrote:
> 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?

Maybe your system is already well minimized and these relaxations are 
not doing anything useful. Also, be sure to use the terminology of 
constraints and restraints correctly.

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