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