# Energy minimization with lone pair

**URL:** <https://gromacs.bioexcel.eu/t/energy-minimization-with-lone-pair/7518>\
**Category:** User discussions\
**Created:** [October 31, 2023, 4:23pm UTC](https://gromacs.bioexcel.eu/t/energy-minimization-with-lone-pair/7518 "2023-10-31T16:23:30Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Alexandra](https://avatars.discourse-cdn.com/v4/letter/a/e68b1a/32.png) [@Alexandra](https://gromacs.bioexcel.eu/u/Alexandra)\
**Post date:** [October 31, 2023, 4:23pm UTC](https://gromacs.bioexcel.eu/t/energy-minimization-with-lone-pair/7518/1 "2023-10-31T16:23:30Z")

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Hi all, a new GROMACS user here. I am using CHARM36 for protein/ligand complex. The ligand has a chlorine atom and CGenFF adds LPH atom and the following line in the topology file:  
LONEPAIR COLI LP1 CL C1 DIST 1.6400 SCAL 0.0.

Salvation and adding ions goes through. When I am trying to do complex structure energy minimization, I get the following warning:  
WARNING 1 [file em.mdp]:  
The largest distance between excluded atoms is 1.398 nm, which is larger  
than the cut-off distance. This will lead to missing long-range  
corrections in the forces and energies. If you expect that minimization  
will bring such distances within the cut-off, you can ignore this warning.

I assume the problem is the lone pair. How do I solve this problem? Can I increase rcoulomb?  
The minimization mdp file is below:

; Parameters describing what to do, when to stop and what to save  
integrator = steep ; Algorithm (steep = steepest descent minimization)  
emtol = 1000.0 ; Stop minimization when the maximum force \< 10.0 kJ/mol  
emstep = 0.01 ; Energy step size  
nsteps = 50000 ; Maximum number of (minimization) steps to perform

; 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  
ns\_type = grid ; Method to determine neighbor list (simple, grid)  
rlist = 1.2 ; Cut-off for making neighbor list (short range forces)  
coulombtype = PME ; Treatment of long range electrostatic interactions  
rcoulomb = 1.2 ; long range electrostatic cut-off  
vdwtype = cutoff  
vdw-modifier = force-switch  
rvdw-switch = 1.0  
rvdw = 1.2 ; long range Van der Waals cut-off  
pbc = xyz ; Periodic Boundary Conditions  
DispCorr = no

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**Author:** ![Christian](https://avatars.discourse-cdn.com/v4/letter/c/b2d939/32.png) [@Christian](https://gromacs.bioexcel.eu/u/Christian)\
**Post date:** [July 25, 2024, 3:08pm UTC](https://gromacs.bioexcel.eu/t/energy-minimization-with-lone-pair/7518/2 "2024-07-25T15:08:43Z")

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Hi Alexandra,  
I am having the same issue with a lone pair on a chlorine atom on my ligand generated by CHARMM-GUI. Did you ever solve this? I am currently trying to increase the rcoulomb to bigger than the distance excluded distance for all the minimization/equilibration steps as was suggested at the end of this thread ([link](https://gromacs.bioexcel.eu/t/the-largest-distance-between-excluded-atoms-is-1-725-nm-which-is-larger-than-the-cut-off-distance/4153/8)). But I’m not sure if this is a good idea.