Frozen beads - no movements

GROMACS version: 2024.4

Hi everyone,
I have made a coarse grained membrane and added antibiotics to it
The antibiotics move through the PBC and will have interactions with both sides of the membrane
I don’t want that because it is not what we are currently looking for in our lab
so I put position restrains on only one layer on water to make a “frozen water layer” to stop the antibiotics moving and reaching the other side (to basically force them to interact with one side only)
The problem is that this position restraint is being applied on everything.
I checked the itps I had and only that frozen water layer had the POSRES
Below, you would see my mdp.
Could anybody help me with what’s wrong with my membrane?
Thank you!!

the mdp file:
;
; STANDARD MD INPUT OPTIONS FOR MARTINI 2.x
; Updated 15 Jul 2015 by DdJ
;
; for use with GROMACS 5
; For a thorough comparison of different mdp options in combination with the Martini force field, see:
; D.H. de Jong et al., Martini straight: boosting performance using a shorter cutoff and GPUs, submitted.

title = Martini

; TIMESTEP IN MARTINI
; Most simulations are numerically stable with dt=40 fs,
; however better energy conservation is achieved using a
; 20-30 fs timestep.
; Time steps smaller than 20 fs are not required unless specifically stated in the itp file.

define = -DPOSRES

integrator = md
dt = 0.01 ; 10 fs timestep
nsteps = 10000000 ; 100 ns total simulation time
nstcomm = 100

nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstenergy = 1000
nstxout-compressed = 5000
compressed-x-precision = 100
compressed-x-grps =
energygrps = Protein_Membrane Solvent

; NEIGHBOURLIST and MARTINI
; To achieve faster simulations in combination with the Verlet-neighborlist
; scheme, Martini can be simulated with a straight cutoff. In order to
; do so, the cutoff distance is reduced 1.1 nm.
; Neighborlist length should be optimized depending on your hardware setup:
; updating ever 20 steps should be fine for classic systems, while updating
; every 30-40 steps might be better for GPU based systems.
; The Verlet neighborlist scheme will automatically choose a proper neighborlist
; length, based on a energy drift tolerance.
;
; Coulomb interactions can alternatively be treated using a reaction-field,
; giving slightly better properties.
; Please realize that electrostVatic interactions in the Martini model are
; not considered to be very accurate to begin with, especially as the
; screening in the system is set to be uniform across the system with
; a screening constant of 15. When using PME, please make sure your
; system properties are still reasonable.
;
; With the polarizable water model, the relative electrostatic screening
; (epsilon_r) should have a value of 2.5, representative of a low-dielectric
; apolar solvent. The polarizable water itself will perform the explicit screening
; in aqueous environment. In this case, the use of PME is more realistic.

cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005

coulombtype = reaction-field
rcoulomb = 1.1
epsilon_r = 15 ;2.5 (with polarizable water)
epsilon_rf = 0
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.1

; MARTINI and TEMPERATURE/PRESSURE
; normal temperature and pressure coupling schemes can be used.
; It is recommended to couple individual groups in your system separately.
; Good temperature control can be achieved with the velocity rescale (V-rescale)
; thermostat using a coupling constant of the order of 1 ps. Even better
; temperature control can be achieved by reducing the temperature coupling
; constant to 0.1 ps, although with such tight coupling (approaching
; the time step) one can no longer speak of a weak-coupling scheme.
; We therefore recommend a coupling time constant of at least 0.5 ps.
; The Berendsen thermostat is less suited since it does not give
; a well described thermodynamic ensemble.
;
; Pressure can be controlled with the Parrinello-Rahman barostat,
; with a coupling constant in the range 4-8 ps and typical compressibility
; in the order of 10e-4 - 10e-5 bar-1. Note that, for equilibration purposes,
; the Berendsen barostat probably gives better results, as the Parrinello-
; Rahman is prone to oscillating behaviour. For bilayer systems the pressure
; coupling should be done semiisotropic.

tcoupl = v-rescale
tc-grps = Protein_Membrane Solvent
tau_t = 1.0 1.0
ref_t = 310 310

pcoupl = Berendsen
pcoupltype = semiisotropic
tau_p = 12
compressibility = 3e-4 3e-4 3e-4
ref_p = 1.0 1.0 1.0
refcoord-scaling = all

gen_vel = yes
gen_temp = 310
gen_seed = -1

; MARTINI and CONSTRAINTS
; for ring systems and stiff bonds constraints are defined
; which are best handled using Lincs.

constraints = none
constraint_algorithm = Lincs
lincs_order = 8
lincs_warnangle = 90
lincs_iter = 2

the FW.itp:
[ moleculetype ]
; molname nrexcl
FW 1

[ atoms ]
;id type resnr residu atom cgnr charge
1 FW 1 FW FW 1 0

[position-restraints]
#ifdef POSRES
1 1 1000000 1000000 1000000

Have you tried making sure that your topology file includes the position restraints rather than just in the mdp file?
When I add restraints to, for example carbon alphas of some amino acids, i include the restraints in the respective chains’ topology file.

Hi,
Thank you for your help!

my itp file is like below:
the FW.itp:
[ moleculetype ]
; molname nrexcl
FW 1

[ atoms ]
;id type resnr residu atom cgnr charge
1 FW 1 FW FW 1 0

[position-restraints]
#ifdef POSRES
1 1 1000000 1000000 1000000


As an update, I have 3reps which 2 of them worked fine and now are running for production.
This problem is only for one of the reps.
I tried startign from scratch with the itps and mdps of the ones that worked (tried restarting from scratch more than 5 times )
I don’t know what I did but in my 6th try, it worked only up until before a certain step of equilibration with the mdp like below. It submits the jobs but gets stuck at step 0.


the 20fs timestep mdp:
;
; STANDARD MD INPUT OPTIONS FOR MARTINI 2.x
; Updated 15 Jul 2015 by DdJ
;
; for use with GROMACS 5
; For a thorough comparison of different mdp options in combination with the Martini force field, see:
; D.H. de Jong et al., Martini straight: boosting performance using a shorter cutoff and GPUs, submitted.

title = Martini

; TIMESTEP IN MARTINI
; Most simulations are numerically stable with dt=40 fs,
; however better energy conservation is achieved using a
; 20-30 fs timestep.
; Time steps smaller than 20 fs are not required unless specifically stated in the itp file.

define = -DPOSRES

integrator = md
dt = 0.02
nsteps = 10000000
nstcomm = 100

nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstenergy = 1000
nstxout-compressed = 5000
compressed-x-precision = 100
compressed-x-grps =
energygrps = Protein_Membrane Solvent

; NEIGHBOURLIST and MARTINI
; To achieve faster simulations in combination with the Verlet-neighborlist
; scheme, Martini can be simulated with a straight cutoff. In order to
; do so, the cutoff distance is reduced 1.1 nm.
; Neighborlist length should be optimized depending on your hardware setup:
; updating ever 20 steps should be fine for classic systems, while updating
; every 30-40 steps might be better for GPU based systems.
; The Verlet neighborlist scheme will automatically choose a proper neighborlist
; length, based on a energy drift tolerance.
;
; Coulomb interactions can alternatively be treated using a reaction-field,
; giving slightly better properties.
; Please realize that electrostVatic interactions in the Martini model are
; not considered to be very accurate to begin with, especially as the
; screening in the system is set to be uniform across the system with
; a screening constant of 15. When using PME, please make sure your
; system properties are still reasonable.
;
; With the polarizable water model, the relative electrostatic screening
; (epsilon_r) should have a value of 2.5, representative of a low-dielectric
; apolar solvent. The polarizable water itself will perform the explicit screening
; in aqueous environment. In this case, the use of PME is more realistic.

cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005

coulombtype = reaction-field
rcoulomb = 1.1
epsilon_r = 15 ;2.5 (with polarizable water)
epsilon_rf = 0
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.1

; MARTINI and TEMPERATURE/PRESSURE
; normal temperature and pressure coupling schemes can be used.
; It is recommended to couple individual groups in your system separately.
; Good temperature control can be achieved with the velocity rescale (V-rescale)
; thermostat using a coupling constant of the order of 1 ps. Even better
; temperature control can be achieved by reducing the temperature coupling
; constant to 0.1 ps, although with such tight coupling (approaching
; the time step) one can no longer speak of a weak-coupling scheme.
; We therefore recommend a coupling time constant of at least 0.5 ps.
; The Berendsen thermostat is less suited since it does not give
; a well described thermodynamic ensemble.
;
; Pressure can be controlled with the Parrinello-Rahman barostat,
; with a coupling constant in the range 4-8 ps and typical compressibility
; in the order of 10e-4 - 10e-5 bar-1. Note that, for equilibration purposes,
; the Berendsen barostat probably gives better results, as the Parrinello-
; Rahman is prone to oscillating behaviour. For bilayer systems the pressure
; coupling should be done semiisotropic.

tcoupl = v-rescale
tc-grps = Protein_Membrane Solvent
tau_t = 1.0 1.0
ref_t = 310 310

pcoupl = Berendsen
pcoupltype = semiisotropic
tau_p = 12
compressibility = 3e-4 3e-4 3e-4
ref_p = 1.0 1.0 1.0
refcoord-scaling = all

gen_vel = yes
gen_temp = 310
gen_seed = -1

; MARTINI and CONSTRAINTS
; for ring systems and stiff bonds constraints are defined
; which are best handled using Lincs.

constraints = none
constraint_algorithm = Lincs
lincs_order = 8
lincs_warnangle = 90
lincs_iter = 8;
; STANDARD MD INPUT OPTIONS FOR MARTINI 2.x
; Updated 15 Jul 2015 by DdJ
;
; for use with GROMACS 5
; For a thorough comparison of different mdp options in combination with the Martini force field, see:
; D.H. de Jong et al., Martini straight: boosting performance using a shorter cutoff and GPUs, submitted.

title = Martini

; TIMESTEP IN MARTINI
; Most simulations are numerically stable with dt=40 fs,
; however better energy conservation is achieved using a
; 20-30 fs timestep.
; Time steps smaller than 20 fs are not required unless specifically stated in the itp file.

define = -DPOSRES

integrator = md
dt = 0.02
nsteps = 10000000
nstcomm = 100

nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstenergy = 1000
nstxout-compressed = 5000
compressed-x-precision = 100
compressed-x-grps =
energygrps = Protein_Membrane Solvent

; NEIGHBOURLIST and MARTINI
; To achieve faster simulations in combination with the Verlet-neighborlist
; scheme, Martini can be simulated with a straight cutoff. In order to
; do so, the cutoff distance is reduced 1.1 nm.
; Neighborlist length should be optimized depending on your hardware setup:
; updating ever 20 steps should be fine for classic systems, while updating
; every 30-40 steps might be better for GPU based systems.
; The Verlet neighborlist scheme will automatically choose a proper neighborlist
; length, based on a energy drift tolerance.
;
; Coulomb interactions can alternatively be treated using a reaction-field,
; giving slightly better properties.
; Please realize that electrostVatic interactions in the Martini model are
; not considered to be very accurate to begin with, especially as the
; screening in the system is set to be uniform across the system with
; a screening constant of 15. When using PME, please make sure your
; system properties are still reasonable.
;
; With the polarizable water model, the relative electrostatic screening
; (epsilon_r) should have a value of 2.5, representative of a low-dielectric
; apolar solvent. The polarizable water itself will perform the explicit screening
; in aqueous environment. In this case, the use of PME is more realistic.

cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005

coulombtype = reaction-field
rcoulomb = 1.1
epsilon_r = 15 ;2.5 (with polarizable water)
epsilon_rf = 0
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.1

; MARTINI and TEMPERATURE/PRESSURE
; normal temperature and pressure coupling schemes can be used.
; It is recommended to couple individual groups in your system separately.
; Good temperature control can be achieved with the velocity rescale (V-rescale)
; thermostat using a coupling constant of the order of 1 ps. Even better
; temperature control can be achieved by reducing the temperature coupling
; constant to 0.1 ps, although with such tight coupling (approaching
; the time step) one can no longer speak of a weak-coupling scheme.
; We therefore recommend a coupling time constant of at least 0.5 ps.
; The Berendsen thermostat is less suited since it does not give
; a well described thermodynamic ensemble.
;
; Pressure can be controlled with the Parrinello-Rahman barostat,
; with a coupling constant in the range 4-8 ps and typical compressibility
; in the order of 10e-4 - 10e-5 bar-1. Note that, for equilibration purposes,
; the Berendsen barostat probably gives better results, as the Parrinello-
; Rahman is prone to oscillating behaviour. For bilayer systems the pressure
; coupling should be done semiisotropic.

tcoupl = v-rescale
tc-grps = Protein_Membrane Solvent
tau_t = 1.0 1.0
ref_t = 310 310

pcoupl = Berendsen
pcoupltype = semiisotropic
tau_p = 12
compressibility = 3e-4 3e-4 3e-4
ref_p = 1.0 1.0 1.0
refcoord-scaling = all

gen_vel = yes
gen_temp = 310
gen_seed = -1

; MARTINI and CONSTRAINTS
; for ring systems and stiff bonds constraints are defined
; which are best handled using Lincs.

constraints = none
constraint_algorithm = Lincs
lincs_order = 8
lincs_warnangle = 90
lincs_iter = 8