GROMACS version: 2023.2

GROMACS modification: Yes/No

Hello and good day,

I am running some cycles of NVT-NPT for swelling procedures on a membrane. Each cycle goes like this

NVT for 250 ps with T goes from 300-600 C

NVT for 500 ps with T at 600 C

NVT for 250 ps with T goes from 600-300 C

NVT for 1000 ps with T at 300 C

and finally an NPT for 500 ps with T 300 C and P at 1 bar

It goes well for the first cycles, but at the second cycle when it reaches to generate the .tpr file for the NPT, I get the following error.

```
There were 2 WARNINGs
[nas-Precision-7820-Tower:81671] *** Process received signal ***
[nas-Precision-7820-Tower:81671] Signal: Segmentation fault (11)
[nas-Precision-7820-Tower:81671] Signal code: Invalid permissions (2)
[nas-Precision-7820-Tower:81671] Failing at address: 0x200000008
[nas-Precision-7820-Tower:81671] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x7fd0f7a42520]
[nas-Precision-7820-Tower:81671] [ 1] /home/nas/Desktop/gromacs-2023.2/build/bin/../lib/libgromacs_mpi.so.8(_ZN22PreprocessingAtomTypesD1Ev+0x113)[0x7fd0f8a07163]
[nas-Precision-7820-Tower:81671] [ 2] /home/nas/Desktop/gromacs-2023.2/build/bin/../lib/libgromacs_mpi.so.8(_Z10gmx_gromppiPPc+0x5d9e)[0x7fd0f8a2386e]
[nas-Precision-7820-Tower:81671] [ 3] /home/nas/Desktop/gromacs-2023.2/build/bin/../lib/libgromacs_mpi.so.8(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x36d)[0x7fd0f869d5bd]
[nas-Precision-7820-Tower:81671] [ 4] gmx_mpi(+0x7e30)[0x56267143be30]
[nas-Precision-7820-Tower:81671] [ 5] /lib/x86_64-linux-gnu/libc.so.6(+0x29d90)[0x7fd0f7a29d90]
[nas-Precision-7820-Tower:81671] [ 6] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80)[0x7fd0f7a29e40]
[nas-Precision-7820-Tower:81671] [ 7] gmx_mpi(+0x7eb5)[0x56267143beb5]
[nas-Precision-7820-Tower:81671] *** End of error message ***
Segmentation fault (core dumped)
```

The NPT input is the following

title = NPT equilibration at 300 K

; Run parameters

integrator = md ; leap-frog integrator

nsteps = 500000 ; 500000 * 0.001 fs = 500 ps

dt = 0.001 ; 1 fs

; Output control

nstxout = 500 ; save coordinates every 1.0 ps

nstvout = 500 ; save velocities every 1.0 ps

nstenergy = 500 ; save energies every 1.0 ps

nstlog = 500 ; update log file every 1.0 ps

; Bond parameters

continuation = yes ; First MD run, gen-vel=yes

;constraint_algorithm = lincs ; No constraints

constraints = none ; No constraints

; Nonbonded settings

cutoff-scheme = Verlet ; Buffered neighbor searching

;verlet-buffer-tolerance = 0.1

ns_type = grid ; search neighboring grid cells

nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme

rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)

rvdw = 1.2 ; short-range van der Waals cutoff (in nm)

DispCorr = EnerPres ; account for cut-off vdW scheme

; Electrostatics

coulombtype = PME ; Cutoff for electrostatics

pme_order = 4 ; cubic interpolation

fourierspacing = 0.12 ; grid spacing for FFT

; Temperature coupling is on

tcoupl = V-rescale ; V-rescale thermostat

tc-grps = system ; two coupling groups - more accurate

tau_t = 0.5 ; time constant, in ps (adjusted)

ref_t = 300 ; reference temperature, one for each group, in K

; Pressure coupling is on

pcoupl = Berendsen ;Pressure coupling on in NPT (changed to Berendsen)

pcoupltype = semiisotropic ; uniform scaling of box vectors

tau_p = 2.0 ; time constant, in ps (adjusted)

ref_p = 1.0 1.0 ; reference pressure, in bar

compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility of water, bar^-1

; Periodic boundary conditions

pbc = xy ; 2-D PBC (only x and y)

nwall = 2 ; Two walls for confinement

wall-atomtype = ljw ljw ; Wall atom types

wall-type = 12-6 ; Wall potential type

wall-r-linpot = 0.1 ; Linear potential distance from the wall

ewald-geometry = 3dc ; Ewald summation geometry

; Velocity generation

gen_vel = no ; Velocity generation is off