GROMACS version:
GROMACS modification: Yes/No
Yes
Brief description of tools/files:
GROMACS/2024.3-cpeAMD-24.03-PLUMED-2.9.3-noPythonrocm
I am running various membane protein systems with 2 different ligands with plumed in the fluid phase. I am using new version of GROMACs so using V-rescale thermostat and C-rescale barostat. I didn’t see this issue running a different ligand using CUDA but that might be futile. After equilibration I have a PCB box of around 9.22180 9.22180 12.68893. However in two replicas of 1 ligand after about 50 ns they start to blow up vertically and shrink in the x and y direction slightly to 8.02553 8.02553 16.53997. For my other system it is not as drastic as it starts with PBC of 9.19547 9.19547 10.84072 or some configurations of 8.67225 8.67225 10.54320 but then can end after 50 or 100 ns at 7.97068 7.97068 12.35322. I have below my .mdp file as well as the walls and METAD from my plumed files. If you need images let me know but its obvious to see from the first change of 9.22180 9.22180 12.68893 to 8.02553 8.02553 16.53997 my membrane system starts to look like a column in the z-direction.
.mdp
integrator = md
dt = 0.002
nsteps = 50000000
xtc-precision = 1000000
nstxtcout = 5000
nstvout = 50000
nstfout = 50000
nstcalcenergy = 1000
nstenergy = 1000
nstlog = 1000
;
cutoff-scheme = Verlet
nstlist = 20
rlist = 1.2
vdwtype = Cut-off
vdw-modifier = Force-switch
rvdw_switch = 1.0
rvdw = 1.2
coulombtype = pme
rcoulomb = 1.2
;
tcoupl = V-rescale
tc_grps = System
tau_t = 1.0
ref_t = 323.15
;
pcoupl = C-rescale
pcoupltype = semiisotropic
tau_p = 5.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
;
constraints = h-bonds
constraint_algorithm = LINCS
continuation = yes
;
nstcomm = 100
comm_mode = linear
comm_grps = SOLU_MEMB SOLV
plumed.dat
# WALLS
lwall: LOWER_WALLS ARG=onaxis AT=0.0 KAPPA=50.0 EXP=2 EPS=1
uwall: UPPER_WALLS ARG=onaxis,fromaxis AT=37.0,7.0 KAPPA=50.0,50.0 EXP=2,2 EPS=1,1
# Protein mantainance
uwall1: UPPER_WALLS ARG=dk AT=1.0 KAPPA=50.0 EXP=2 EPS=1
# Bias on axis and fromaxis
METAD ...
ARG=onaxis,fromaxis
PACE=2000
HEIGHT=0.25
BIASFACTOR=15
SIGMA=0.25,0.25
GRID_MIN=-2.0,0.0
GRID_MAX=40.0,8.0
GRID_BIN=500,100
WALKERS_N=3
WALKERS_ID=0
WALKERS_DIR=../WALKERS/
WALKERS_RSTRIDE=500
TEMP=323.15
LABEL=metad
... METAD