NPT fatal error

User discussions
1

GROMACS version: 2021.4
GROMACS modification: Yes/No
Here post your question : While running the NPT equilibration for a protein-cyclohexane system at temperature of 310K (charmm36 ff), I am getting the following error
Program: gmx mdrun, version 2021.4-Ubuntu-2021.4-2
Source file: src/gromacs/domdec/cellsizes.cpp (line 143)
MPI rank: 0 (out of 20)
Fatal error:
The X-size of the box (5.953902) times the triclinic skew factor (1.000000) is
smaller than the number of DD cells (4) times the smallest allowed cell size
(1.488750).

The following is npt.mdp file for your reference:
title = charmm36 Protein-CYHE system NPT equilibration
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 2500000 ; 2 * 2500000 = 5000 ps
dt = 0.002 ; 2 fs
; Output control
nstenergy = 500 ; save energies every 1.0 ps
nstlog = 500 ; update log file every 1.0 ps
nstxout-compressed = 500 ; save coordinates every 1.0 ps
; Bond parameters
continuation = yes ; continuing from NVT
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds to H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighbor searching and vdW
cutoff-scheme = Verlet
ns_type = grid ; search neighboring grid cells
nstlist = 20 ; largely irrelevant with Verlet
rlist = 1.2
vdwtype = cutoff
vdw-modifier = force-switch
rvdw-switch = 1.0
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
rcoulomb = 1.2
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more accurate
tau_t = 1.0 1.0 ; time constant, in ps
ref_t = 310 310 ; reference temperature, one for each group, in K
; Pressure coupling
pcoupl = C-rescale ; pressure coupling is on for NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 5.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
refcoord_scaling = com
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction is not used for proteins with the C36 additive FF
DispCorr = no
; Velocity generation
gen_vel = no ; velocity generation off after NVT

I used these npt.mdp parameters for the same system at 290K temperature, it worked. I have to compare the 2 systems.

Can anyone please help me resolve this issue?

2

The minimum cell size is large. I don’t understand why this is so high. Could you post the lines at the beginning of the log file that pertain to the domain decomposition and detection of distances that affect this?

3

Did you use as many MPI ranks (20) when you ran the 290K simulation?
How many atoms are there in the system? Does it work if you run one, two or four MPI ranks?

4

I tried to run the NPT equilibration again and again, and it finally got completed without any error. But I got this error again for 300K.
I have attached the npt.log file.
npt.log (1.6 MB)

5

Does it help if you use fewer MPI ranks? Do you really need that many? I think 2 or 4 would be enough, i.e., 5-10 logical cores per MPI rank.

6

Yes, as I am comparing the system at different temperatures of 290K, 300K and 310K, so all parameters of equilibration (except time step) is kept same. But I tried running the npt equilibration again (twice), and it finally got completed without any error, but then again I got same error for 300K.

7

I have been using all the available cores on my PC. I will try using fewer and see if it works. Thank you for helping.

8

You can still use all available cores, but you don’t need to use separate MPI ranks for them. Try with -ntmpi 2.

9

I see now that the unusual situation is that your box volume decreases by a factor 2.6. This makes the domain decomposition smaller than what the initial margin accounted for.

Adding the option -dds 0.6 to mdrun should give sufficient margin. But I would expect that continuing your run from the last checkpoint file should also work, even without the -dds option.