[gmx-users] a question in energy minimization step

[Mark Abraham]

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.

Mark
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