Energy minimization of an interfacial system

User discussions
1

GROMACS version: 2022
GROMACS modification: No
Dear All,
I am trying to get the energy minimized structure of a 10x10 Platinum surface with 3 layers along with a single ion pair ionic liquid (1-butyl-3-methylimidazolium tetraflouroborate). During the energy minimization, it shows some LINCS warning, printing the atoms and bonds that rotated more than 30 degrees, and the potential energy comes up to be infinity, with forces being very high. Kindly help on this matter. I am pasting the em.mdp file content here

integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep = 0.01 ; Minimization step size
nsteps = 100000 ; Maximum number of (minimization) steps to perform
nstlog = 20
nstxout = 1

;Frozen group
;energygrps = ICE
freezegrps = Pt
freezedim = Y Y Y

; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 2 ; 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 = 1.2 ; Short-range electrostatic cut-off
rvdw = 1.2 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions

Arka Prava Sarkar
Research Scholar
IIT Kharagpur

2

@APSDft did you solved this issue of bonds rotation.?

3

Recheck your ff files carefully. specially for the IL. This is very common also simulate in bulk and see if you can replicate all the properties of [BMIM] [BF4].

Thanks,
Devargya

4

what kind of problem are you facing??

Thanks,
Devargya

5

I have considered 1 molecule of span80. Energy is minimized upto possible extent. At minimum energy after visualization came know that hydrogen of 1 alcphol group come to close to oxgyen of another alcohol group. After this in NVT run, system shows that angles btw two atoms are rotating more than 30 degree. Error: segmentation fault.

Initial optimized structure and itp file downloaded from automated topology builder platform.

Thanks in advance

6

Try to replicate from Published resources. you can have a look at this paper.

https://pubs.acs.org/doi/10.1021/acs.jpcb.8b03945

You can find the ff files and structure of span80 in the supplementary information of this work.

Thanks,
Devargya