PBC changing drastically vertical in replicas of membrane protein with plumed

User discussions
1

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 500 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 ligand it is not as drastic

2

I think this is a question for Plumed, not GROMACS.

3

Sorry I posted in wrong spot and post here now. It also happens without plumed flag. Initially start at 10.15726 10.15726 11.86791 after equilibration and by 27 nanoseconds goes to 8.82787 8.82787 15.53842.

4

What are you mdp settings for pressure coupling?

5

I am using this which is basically defaults from Charmm-GUI:

pcoupl                  = C-rescale
pcoupltype              = semiisotropic
tau_p                   = 5.0
compressibility         = 4.5e-5  4.5e-5
ref_p                   = 1.0     1.0

This is the entire mdp file:

integrator              = md
dt                      = 0.002
nsteps                  = 50000000
xtc-precision           = 1000000
;nstxout                 = 50000
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
6

The simplest explanation would be that your membrane doesn’t have the correct area in the initial configuration.

7

Thanks, so sorry I indicated that it also happened without plumed but I was checking the wrong file. It seems to only happen in this one system and with plumed so I will keep trying and if still persists email plumed.