# Energy Minimization of protein (PDB)

**URL:** <https://gromacs.bioexcel.eu/t/energy-minimization-of-protein-pdb/10028>\
**Category:** User discussions\
**Tags:** mdp-parameters\
**Created:** [August 28, 2024, 6:20pm UTC](https://gromacs.bioexcel.eu/t/energy-minimization-of-protein-pdb/10028 "2024-08-28T18:20:32Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![maham](https://avatars.discourse-cdn.com/v4/letter/m/c77e96/32.png) [@maham](https://gromacs.bioexcel.eu/u/maham)\
**Post date:** [August 28, 2024, 6:20pm UTC](https://gromacs.bioexcel.eu/t/energy-minimization-of-protein-pdb/10028/1 "2024-08-28T18:20:32Z")

</div>

GROMACS version:  
GROMACS modification: Yes/No  
Here post your question  
I am trying to simulate a protein having 2 chains. I have used Charmm 36 forcefield and following is the em.mdp parameters that i am using for minimization.  
integrator = steep  
emstep = 0.001 ; Minimization step size  
nsteps = 40000 ; Maximum number of (minimization) steps to perform

; Output control  
nstxout = 250 ; save coordinates every 1 ps  
nstvout = 250 ; save velocities every 1 ps  
nstenergy = 250 ; save energies every 1 ps  
nstlog = 250 ; update log file every 1 ps

; Parameters describing how to find the neighbors of each atom and how to calculate the interactions  
nstlist = 1 ; Frequency to update the neighbor list and long range forces  
cutoff-scheme = Verlet ; Buffered neighbor searching  
ns\_type = grid ; Method to determine neighbor list (simple, grid)  
coulombtype = PME ; Treatment of long range electrostatic interactions  
rcoulomb = 1.0 ; Short-range electrostatic cut-off  
rvdw = 1.0 ; Short-range Van der Waals cut-off  
pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions

i am getting this error "Energy minimization has stopped, but the forces have not converged to the  
requested precision Fmax \< 10 (which may not be possible for your system). It  
stopped because the algorithm tried to make a new step whose size was too  
small, or there was no change in the energy since last step. Either way, we  
regard the minimization as converged to within the available machine  
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not  
needed for preparing to run molecular dynamics.

Steepest Descents converged to machine precision in 19223 steps,  
but did not reach the requested Fmax \< 10.  
Potential Energy = -2.3072438e+06  
Maximum force = 1.4922278e+02 on atom 1008  
Norm of force = 2.2953074e+00

```
D O M A I N D E C O M P O S I T I O N S T A T I S T I C S

```

av. #atoms communicated per step for force: 2 x 203895.7  
" . i have even tried multiple values for emsteps. have even used CG algorithm . how to resolve it? I really want the energy minimization of 40 ps.

---

<div class="post-metadata">

**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\
**Post date:** [August 28, 2024, 6:43pm UTC](https://gromacs.bioexcel.eu/t/energy-minimization-of-protein-pdb/10028/2 "2024-08-28T18:43:11Z")

</div>

In my experience an Fmax of 10 kJ/mol/nm is very very small and usually I stop when the force is of the order of 100 to 1000 kJ/mol/nm.

Is there a reason why you are aiming for such a value? Also, why do you want 40ps of minimization? Keep in mind that this is not a real time, as the steepest descent (ideally) pushes for the direction of the minimum of the potential energy, rather than having a real dynamical simulation where you integrate the equation of motion from the set of position, velocities and forces.

---

<div class="post-metadata">

**Author:** ![maham](https://avatars.discourse-cdn.com/v4/letter/m/c77e96/32.png) [@maham](https://gromacs.bioexcel.eu/u/maham)\
**Post date:** [August 29, 2024, 6:22am UTC](https://gromacs.bioexcel.eu/t/energy-minimization-of-protein-pdb/10028/3 "2024-08-29T06:22:23Z")

</div>

i have predicted some structure from alphafold and I want to see the graph of rmsd after 40ps whether it has fully converged or not .

---

<div class="post-metadata">

**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\
**Post date:** [August 30, 2024, 8:22am UTC](https://gromacs.bioexcel.eu/t/energy-minimization-of-protein-pdb/10028/4 "2024-08-30T08:22:21Z")

</div>

I am not completely sure about how to help you, also because I would compute an RMSD on a trajectory from a NPT run rather than from an EM run.

Also I am not really sure you can consider the `nsteps` parameters as a time step when you do energy minimization. This is not the number of time steps you do like when you run a MD sim where you are integrating the equation of motion. This is a steepest descent, the number of steps indicates only the max amount of steps that the system is going to try to perform in space to try to minimize your max force below the threshold you require. The magnitude of the step, which then is translated in an update in positions, is also largely decided by `emstep` and not simply by the velocities and forces on the atoms, like in the classical MD run.