GROMACS version:2021
GROMACS modification: Yes/No
Here post your question
I am getting an error in energy minimisation that forces on the atom is infinite it is suggested to use soft core potentials. when I am using the softcore minimisation I am getting the state B charge and also a warning that the system is not neutral with a note of state B charge of the system. If ignore and run the mdrun I get that error mentioning
Fatal error:
Function type Restricted Angles do not support currently free energy
calculations
Could you explain what it is you are trying to do? Could you post the input mdp file, and a copy-paste (preferably not a snapshot or photo of the screen) of the terminal output? Are you using angle restraints?
I am trying to do the energy minimization it showed force on the atoms is infinite use the soft core potentials for minimization. when I tried that it showed a note state B charge and the warning system was not neutral. Since i already neutralized the system before running normal minimization.
Mdp file:
integrator = steep
emtol = 500.0
nsteps = 100000
nstlist = 10
cutoff-scheme = Verlet
rlist = 1.2
vdwtype = Cut-off
vdw-modifier = Force-switch
rvdw_switch = 1.0
rvdw = 1.2
coulombtype = pme
rcoulomb = 1.2
; Free energy parameters
free-energy = yes
init-lambda = 0.01
sc-alpha = 4
sc-power = 2
sc-coul = yes
nstdhdl = 0
couple-moltype = system
; we are changing both the vdw and the charge. In the initial state, both are on
couple-lambda0 = vdw-q
; in the final state, both are off.
couple-lambda1 = none
couple-intramol = yes
refcoord_scaling = all
for the second system I am getting linics warning in the equilibration so I try to use soft energy minimization for again same state B charge is coming. Looking forward to hear from you. @MagnusL
First, I think you would be better off trying to find why the forces are infinite, without complicating things by using alchemical free energy transformations. Have a close look at the atom(s) you get in the EM output.
However, if your system is very dense/tightly packed and you want to add a molecule to it, you might have to resort to alchemical transformations. Personally I’ve never done it during energy minimization, though, but I’ve read others do so. Can you paste the message that suggests you “to use soft core potentials”? Or is it suggested somewhere else?
Anyhow, turning to your settings … You are running the simulation with interactions scaled down by 1 % and you are not changing that during the simulation. Is that really what you want to do? It would almost only complicate things by introducing alchemical perturbations and make the simulation extremely slow. Are you sure you want to decouple your whole system? I don’t think that’s a good idea. If there is a specific molecule you need to insert - where there is no room for it - decouple that molecule (starting with very low interactions and turn them on gradually). Why are you using sc-alpha = 4? That is not a very common setting. I’ve seen that some people seem to have to use alchemical perturbations to get lipids properly packed. It might work, but I think it would be good if there was a better solution, i.e., a better starting configuration.
I don’t understand why you are getting the message about the net charge, though If the system is neutral in state A and state B is fully decoupled you should not get that message. Do you get it if you use Gromacs 2024.3?
Hi sir, sorry for the delayed response. Actually, I didn’t try the latest version of Gromacs. I will try using that and if the same error persist I will reply in this thread, Thank you sir