Error while running a pull in umbrella sampling

User discussions
1

GROMACS version: 2020.1-Ubuntu-2020.1-1
GROMACS modification: Yes/No
Im running a workflow for an umbrella sampling pulling a ion away from a peptide:

gmx pdb2gmx -f Peptide.pdb -o processed.gro -water tip3p -ff amber14sb

gmx editconf -f processed.gro -o newbox.gro -c -d 3 -bt triclinic

gmx solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro

gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr

echo -e “SOL” | gmx genion -s ions.tpr -o peptide_ions.gro -p topol.top -pname LI -nname CL -neutral -np 1 -nn 1

gmx grompp -f minim.mdp -c peptide_ions.gro -p topol.top -o em.tpr

gmx mdrun -v -deffnm em

gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr

gmx mdrun -deffnm nvt

gmx grompp -f npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -o npt.tpr

gmx mdrun -deffnm npt

gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_01.tpr

gmx mdrun -v -deffnm md_01

gmx grompp -f pull.mdp -c md_01.gro -t md_01.cpt -p topol.top -o pull.tpr

gmx mdrun -v -deffnm pull

almost all the process run well, but when i run the line of code i get this error:
Output error:
starting mdrun ‘Protein in water’
500000 steps, 1000.0 ps.
step 7600, will finish Thu Aug 15 14:02:23 2024vol 0.69 imb F 4% pme/F 0.76

Program: gmx mdrun, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/ewald/pme_redistribute.cpp (line 305)
MPI rank: 29 (out of 48)

Fatal error:
100 particles communicated to PME rank 4 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.

Im attaching below the parameters files. im comitting a mistake somewhere and im not seeing it?
allParameters.mdp (9.8 KB)

2

I notice that under the temperature coupling parameters, you used only a single coupling group for nvt, npt and md, then switched to 2 coupling groups once you got to pull. Typically you would maintain 2 coupling groups for all steps, could you try to see if that would fix the issue?

You could also try plotting the temperature after the nvt step and density after the npt step as is done in the lysozyme tutorial to see if there’s some issue with either equilibration step, it looks like you’re using a larger tau_t and tau_p over a longer equilibration time compared to the tutorial, so this would check whether those parameters need adjusting

3

Hello Karis, thanks for your reply, i had change the parameters in my .mdp files to use the coupling groups, also changed the tau_t and tau_p to the values of the tutorial, but im keep getting this error:

Back Off! I just backed up pull.edr to ./#pull.edr.9#
starting mdrun ‘Protein in water’
500000 steps, 1000.0 ps.
step 15400, will finish Sat Aug 17 17:38:49 2024vol 0.91 imb F 2% pme/F 0.68

Program: gmx mdrun, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/ewald/pme_redistribute.cpp (line 305)
MPI rank: 17 (out of 48)

Fatal error:
18 particles communicated to PME rank 2 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.

this is the equilibration temperature plot (seems to be ok, pressure and density looks equilibrated too):

temperature
temperature700×432 5.16 KB

4

Could you copy-paste the notes/warnings/errors from the previous commands (basically all the messages that were output for each command)? Also, could you try adding refcoord_scaling = com under the pressure coupling section of the pull mdp (as is done in this tutorial)?

5

refcoord_scaling = com (added)
Here i let all the output i received from the workflow
log.txt (39.4 KB)

6

Could you try visualizing the pull simulation to see what might be going wrong? It might be that the parameters aren’t wrong but the ion is just getting stuck somewhere even as the force from the pull increases over time

7

Do you have a membrane in your system? The mdp parameters are for a membrane system, but I guess you do not have a membrane. If you have no membrane you should change the pressure coupling type to isotropic and turn on all dimensions for pulling.