There are no atom pairs for dispersion correction

User discussions
1

GROMACS version: gromacs/2020.1-openmpi-cuda10.1
GROMACS modification: Yes/No

Hello, I am interested to run a simulation for protein in solvent using GROMACS. I am using GROMACS on HPC. Currently, I am facing an issue where during the production MD, the GROMACS job ended with a warning stating " WARNING: There are no atom pairs for dispersion correction". I have tried it using other solvent as well but still getting the same error. This caused my GROMACS job to failed without any results.

May I know what is the issue for this error that I am facing?

The .mdp file for production MD is as follow:

integrator = md ; leap-frog integrator
nsteps = 25000000 ; 50 * 500000 = 50000 ps (50 ns)
dt = 0.002 ; 2 fs
comm_mode = Linear ; remove center of mass translation
nstcomm = 1 ; [steps] frequency of mass motion removal
comm_grps = Protein Non-Protein ; group(s) for center of mass motion removal
; Output control
nstxout = 0 ; suppress bulky .trr file by specifying
nstvout = 0 ; 0 for output frequency of nstxout,
nstfout = 0 ; nstvout, and nstfout
nstenergy = 1000 ; save energies every 2.0 ps
nstlog = 1000 ; update log file every 2.0 ps
nstxtcout = 1000 ; write .xtc trajectory every 2.0 ps
energygrps = Protein Non-Protein
; Bond parameters
continuation = yes ; Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist = 1.0 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
coulomb-modifier = Potential-shift-Verlet
vdw-type = Cut-off
vdw-modifier = Potential-shift-Verlet
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; Velocity generation is off

Thank you very much.

Sincerely,
Raymond

2

Hi,
the warning means that all the Lennart-Jones interactions are zero. That means that the L-J Energy is zero. Is it the case?
Best regards
Alessandra

3

Hi Alessandra,

I think there is no L-J interaction for the simulation. May I know is there any parameter that I need to add into the .mdp file or is there anything I need to specify in order to allow for L-J interaction?

Sincerely,
Raymond

4

Hi,
I do not see any option that prevents LJ calculation in your mdp file.
An option is that LJ parameters are set to zero. LJ parameters are defined in the force field directory that is included in the topology file. Do you get any warning in the pre-processing (gmx grompp)? Do you use a standard force field implementation for protein and solvent?
Kind regards
Alessandra

5

Hi Alessandra,

I did not get any warning during the pre-processing (gmx grompp) where it only appear some notes where it is not significant. I have go through the forcefield directory for amber99sb-ildn where it is the force field that I have implemented for the simulation. I have a view on the forcefield.itp and I have found this:

#define _FF_AMBER
#define _FF_AMBER99SBILDN

[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.5 0.8333

#include “ffnonbonded.itp”
#include “ffbonded.itp”
Is this the file that you said where the LJ parameters were set to zero?

I have used a standard force field implementation for the protein and solvent. For the solvent (methanol), I construct using Avogadro software and auto optimized it using GAFF. Then, I used Gaussian software to undergo frequency and geometric optimization. The output was then brought to Antechamber for RESP fitting and check for missing angle and bond. The solvent.mol2 file was then convert into GROMACS readable file (.gro) using acpype.

Then I tried to simulation the protein and solvent using amber99sb-ildn force field.

Sincerely,
Chan Kam Khong

6

Hi again,
I do not understand where the problem exactly is.
Could you provide me a link with the input files? Thus I can check.
Best regards
Alessandra

7

Hi Alessandra,

I have provide a link to the Dropbox folder that containing all the input files and the pre-processing files. The link is provided here " https://www.dropbox.com/sh/3lk8a81yeawgm0q/AABCpAzmUPZTqkAb9ynmNk7ma?dl=0 ". This is the Dropbox link and feel free to let me know if there is an issue in viewing the files.

All the simulations were done under the force field " amber99sb-ildn “. The error caused the termination with a warning stating " WARNING: There are no atom pairs for dispersion correction”.

Thank you very much.

Sincerely,
Raymond

8

Hi Raymond,
sorry for the late answer. I could not reproduce the error/warning you got. Using the inputs you provided, both gromacs version 2020.1 and 2020.4 run without any errors or warnings.
Could you double check if the version, you used, was really 2020.1, and not 2020?
If you used 2020, ask the cluster admin to update to the current GROMACS version (2020.4).
If you used 2020.1, you can send me the log and tpr file of the run that gave the warning.

Best regards
Alessandra

9

Hi Alessandra,

Alright I will contact the admin and see if its the issue with the software version.

Thank you very much.

Sincerely,
Raymond