[gmx-users] Energy minimization

Itamar Kass ikass at cc.huji.ac.il
Mon Jan 10 16:15:14 CET 2005

On Jan 10, 2005, at 4:36 PM, Andrea Bacconi wrote:

>  Hallo everybody,
>  I'm very new in the use of Gromacs 3.2 and I would like to ask people 
> with more experience than me about the energy minimization procedure.
>  I'm trying to minimize the energy of a protein I obtained by homology 
> modelling (it's about 500 aa) following a paper where the authors did 
> a work similar to the one I'm doing now. My problem is simple:
>  in this paper authors say : "Electrostatic forces were calculated 
> with the particle-mesh Ewald algorithm. Initial energy minimization 
> was done with the steep descent algorithm (1000 steps) followed by 
> conjugate gradient to a maximum force of 0.1 Kj mol-1 nm-1." do they 
> mean that in the same em.mdp script they used both s.d and c.g one 
> after the other?

   If they work with GROMACS they used two stages process, with two 

> I all the tutorials I found the energy minimization was done by using 
> either one or the other algorithm, or using the nstcgsteep option with 
> c.g as main algorithm, so how can you use (if its possible) one 
> algorithm and then the other in the same em.mdp script?

    Use the output from the steep run as input to the CG run.

>  Minimizing the protein energy using Gromacs with single precision, no 
> constraints, cg and nstcgsteep gives an Fmax of 50 Kj mol-1 nm-1 , if 
> I go below this value the system converge to machine precison but not 
> to the requested Fmax (lets say 10 Kj mol-1 nm-1 ).
>  My goal is to improve the reached Fmax up to the paper's level, if 
> it's possible, and then run a  full molecular dinamic simulation in 
> water.

    This happens, do full MD with this structure, do not forget to 
solvate the protein properly (adding water;EM ; MD where the protein it 
PR ; full MD).

> Thank you for your attention and help
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