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GROMACS Version 5
- da294
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9 years 6 months ago - 9 years 6 months ago #4098
by da294
GROMACS Version 5 was created by da294
Hello,
I have been running Martini simulations with GROMACS 4.x using an mdp file based on that provided in the downloads section (I have copied it below). Aside from warnings, it worked fine with GROMACS 4.x. However, when I try to run it with GROMACS 5, I get the following errors:
1) With Verlet lists only cut-off, reaction-field, PME and Ewald
electrostatics are supported
2) Explicit switch/shift coulomb interactions cannot be used in combination
with a secondary coulomb-modifier.
I understand that the mdp example specifically states that it is for GROMACS 4.5/4.6, however I have not found an example for GROMACS 5.0. Is there any example available for GROMACS 5.0, or is there a way to modify the current one to work with 5.0?
Thanks for your time,
David
____________________________________________________________________
; STANDARD MD INPUT OPTIONS FOR MARTINI 2.x
; Updated 02 feb 2013 by DdJ
;
; for use with GROMACS 4.5/4.6
;
title = Martini
; TIMESTEP IN MARTINI
; Most simulations are numerically stable
; with dt=40 fs, some (especially rings and polarizable water) require 20-30 fs.
; Note that time steps of 40 fs and larger may create local heating or
; cooling in your system. Although the use of a heat bath will globally
; remove this effect, it is advised to check consistency of
; your results for somewhat smaller time steps in the range 20-30 fs.
; Time steps exceeding 40 fs should not be used; time steps smaller
; than 20 fs are also not required unless specifically stated in the itp file.
integrator = md
dt = 0.03 ; changed from 0.02 to 0.04 for new chol
nsteps = 1250000000
nstcomm = 10
comm-grps =
nstxout = 250000
nstvout = 250000
nstfout = 0
nstlog = 250000
nstenergy = 250000
nstxtcout = 0
xtc_precision = 0
xtc-grps =
energygrps = DPPC DUPC CHOL W
; NEIGHBOURLIST and MARTINI
; Due to the use of shifted potentials, the noise generated
; from particles leaving/entering the neighbour list is not so large,
; even when large time steps are being used. In practice, once every
; ten steps works fine with a neighborlist cutoff that is equal to the
; non-bonded cutoff (1.2 nm). However, to improve energy conservation
; or to avoid local heating/cooling, you may increase the update frequency
; and/or enlarge the neighbourlist cut-off (to 1.4 nm). The latter option
; is computationally less expensive and leads to improved energy conservation
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.2
; MARTINI and NONBONDED
; Standard cut-off schemes are used for the non-bonded interactions
; in the Martini model: LJ interactions are shifted to zero in the
; range 0.9-1.2 nm, and electrostatic interactions in the range 0.0-1.2 nm.
; The treatment of the non-bonded cut-offs is considered to be part of
; the force field parameterization, so we recommend not to touch these
; values as they will alter the overall balance of the force field.
; In principle you can include long range electrostatics through the use
; of PME, which could be more realistic in certain applications
; Please realize that electrostatic 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.
;
; For use in combination with the Verlet-pairlist algorithm implemented
; in Gromacs 4.6 a straight cutoff in combination with the potential
; modifiers can be used. Although this will change the potential shape,
; preliminary results indicate that forcefield properties do not change a lot
; when the LJ cutoff is reduced to 1.1 nm. Be sure to test the effects for
; your particular system. The advantage is a gain of speed of 50-100%.
coulombtype = Shift ;Reaction_field (for use with Verlet-pairlist) ;PME (especially with polarizable water)
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15 ; 2.5 (with polarizable water)
vdw_type = Shift ;cutoff (for use with Verlet-pairlist)
rvdw_switch = 0.9
rvdw = 1.2 ;1.1 (for use with Verlet-pairlist)
;cutoff-scheme = verlet
;coulomb-modifier = Potential-shift
;vdw-modifier = Potential-shift
;epsilon_rf = 0 ; epsilon_rf = 0 really means epsilon_rf = infinity
;verlet-buffer-drift = 0.005
; 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 10-4 - 10-5 bar-1. Note that, for equilibration purposes,
; the Berendsen thermostat 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 = DPPC DUPC CHOL W
tau_t = 1.0 1.0 1.0 1.0
ref_t = 295 295 295 295
Pcoupl = Berendsen
Pcoupltype = semiisotropic
tau_p = 4.0 4.0 ;parrinello-rahman is more stable with larger tau-p, DdJ, 20130422
compressibility = 5e-5 5e-5
ref_p = 1.0 1.0
gen_vel = yes
gen_temp = 295
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
unconstrained_start = no
lincs_order = 8 ; changed from 4 to 8 for new chol
lincs_iter = 2 ; added for new chol
lincs_warnangle = 30
I have been running Martini simulations with GROMACS 4.x using an mdp file based on that provided in the downloads section (I have copied it below). Aside from warnings, it worked fine with GROMACS 4.x. However, when I try to run it with GROMACS 5, I get the following errors:
1) With Verlet lists only cut-off, reaction-field, PME and Ewald
electrostatics are supported
2) Explicit switch/shift coulomb interactions cannot be used in combination
with a secondary coulomb-modifier.
I understand that the mdp example specifically states that it is for GROMACS 4.5/4.6, however I have not found an example for GROMACS 5.0. Is there any example available for GROMACS 5.0, or is there a way to modify the current one to work with 5.0?
Thanks for your time,
David
____________________________________________________________________
; STANDARD MD INPUT OPTIONS FOR MARTINI 2.x
; Updated 02 feb 2013 by DdJ
;
; for use with GROMACS 4.5/4.6
;
title = Martini
; TIMESTEP IN MARTINI
; Most simulations are numerically stable
; with dt=40 fs, some (especially rings and polarizable water) require 20-30 fs.
; Note that time steps of 40 fs and larger may create local heating or
; cooling in your system. Although the use of a heat bath will globally
; remove this effect, it is advised to check consistency of
; your results for somewhat smaller time steps in the range 20-30 fs.
; Time steps exceeding 40 fs should not be used; time steps smaller
; than 20 fs are also not required unless specifically stated in the itp file.
integrator = md
dt = 0.03 ; changed from 0.02 to 0.04 for new chol
nsteps = 1250000000
nstcomm = 10
comm-grps =
nstxout = 250000
nstvout = 250000
nstfout = 0
nstlog = 250000
nstenergy = 250000
nstxtcout = 0
xtc_precision = 0
xtc-grps =
energygrps = DPPC DUPC CHOL W
; NEIGHBOURLIST and MARTINI
; Due to the use of shifted potentials, the noise generated
; from particles leaving/entering the neighbour list is not so large,
; even when large time steps are being used. In practice, once every
; ten steps works fine with a neighborlist cutoff that is equal to the
; non-bonded cutoff (1.2 nm). However, to improve energy conservation
; or to avoid local heating/cooling, you may increase the update frequency
; and/or enlarge the neighbourlist cut-off (to 1.4 nm). The latter option
; is computationally less expensive and leads to improved energy conservation
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.2
; MARTINI and NONBONDED
; Standard cut-off schemes are used for the non-bonded interactions
; in the Martini model: LJ interactions are shifted to zero in the
; range 0.9-1.2 nm, and electrostatic interactions in the range 0.0-1.2 nm.
; The treatment of the non-bonded cut-offs is considered to be part of
; the force field parameterization, so we recommend not to touch these
; values as they will alter the overall balance of the force field.
; In principle you can include long range electrostatics through the use
; of PME, which could be more realistic in certain applications
; Please realize that electrostatic 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.
;
; For use in combination with the Verlet-pairlist algorithm implemented
; in Gromacs 4.6 a straight cutoff in combination with the potential
; modifiers can be used. Although this will change the potential shape,
; preliminary results indicate that forcefield properties do not change a lot
; when the LJ cutoff is reduced to 1.1 nm. Be sure to test the effects for
; your particular system. The advantage is a gain of speed of 50-100%.
coulombtype = Shift ;Reaction_field (for use with Verlet-pairlist) ;PME (especially with polarizable water)
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15 ; 2.5 (with polarizable water)
vdw_type = Shift ;cutoff (for use with Verlet-pairlist)
rvdw_switch = 0.9
rvdw = 1.2 ;1.1 (for use with Verlet-pairlist)
;cutoff-scheme = verlet
;coulomb-modifier = Potential-shift
;vdw-modifier = Potential-shift
;epsilon_rf = 0 ; epsilon_rf = 0 really means epsilon_rf = infinity
;verlet-buffer-drift = 0.005
; 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 10-4 - 10-5 bar-1. Note that, for equilibration purposes,
; the Berendsen thermostat 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 = DPPC DUPC CHOL W
tau_t = 1.0 1.0 1.0 1.0
ref_t = 295 295 295 295
Pcoupl = Berendsen
Pcoupltype = semiisotropic
tau_p = 4.0 4.0 ;parrinello-rahman is more stable with larger tau-p, DdJ, 20130422
compressibility = 5e-5 5e-5
ref_p = 1.0 1.0
gen_vel = yes
gen_temp = 295
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
unconstrained_start = no
lincs_order = 8 ; changed from 4 to 8 for new chol
lincs_iter = 2 ; added for new chol
lincs_warnangle = 30
Last edit: 9 years 6 months ago by da294. Reason: formatting was wrong
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- xavier
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9 years 6 months ago #4104
by xavier
Replied by xavier on topic GROMACS Version 5
From the warnings it looks like you are not using the default settings of Martini. You are using the Verlet list, which is non-standard for Martini. Although we have made some tests it is not advised to use it without further tests … that you can perform.
You did modify the mod file so it would be better giving it for check.
You did modify the mod file so it would be better giving it for check.
da294 wrote: Hello,
I have been running Martini simulations with GROMACS 4.x using an mdp file based on that provided in the downloads section (I have copied it below). Aside from warnings, it worked fine with GROMACS 4.x. However, when I try to run it with GROMACS 5, I get the following errors:
1) With Verlet lists only cut-off, reaction-field, PME and Ewald
electrostatics are supported
2) Explicit switch/shift coulomb interactions cannot be used in combination
with a secondary coulomb-modifier.
I understand that the mdp example specifically states that it is for GROMACS 4.5/4.6, however I have not found an example for GROMACS 5.0. Is there any example available for GROMACS 5.0, or is there a way to modify the current one to work with 5.0?
Thanks for your time,
David
____________________________________________________________________
; STANDARD MD INPUT OPTIONS FOR MARTINI 2.x
; Updated 02 feb 2013 by DdJ
;
; for use with GROMACS 4.5/4.6
;
title = Martini
; TIMESTEP IN MARTINI
; Most simulations are numerically stable
; with dt=40 fs, some (especially rings and polarizable water) require 20-30 fs.
; Note that time steps of 40 fs and larger may create local heating or
; cooling in your system. Although the use of a heat bath will globally
; remove this effect, it is advised to check consistency of
; your results for somewhat smaller time steps in the range 20-30 fs.
; Time steps exceeding 40 fs should not be used; time steps smaller
; than 20 fs are also not required unless specifically stated in the itp file.
integrator = md
dt = 0.03 ; changed from 0.02 to 0.04 for new chol
nsteps = 1250000000
nstcomm = 10
comm-grps =
nstxout = 250000
nstvout = 250000
nstfout = 0
nstlog = 250000
nstenergy = 250000
nstxtcout = 0
xtc_precision = 0
xtc-grps =
energygrps = DPPC DUPC CHOL W
; NEIGHBOURLIST and MARTINI
; Due to the use of shifted potentials, the noise generated
; from particles leaving/entering the neighbour list is not so large,
; even when large time steps are being used. In practice, once every
; ten steps works fine with a neighborlist cutoff that is equal to the
; non-bonded cutoff (1.2 nm). However, to improve energy conservation
; or to avoid local heating/cooling, you may increase the update frequency
; and/or enlarge the neighbourlist cut-off (to 1.4 nm). The latter option
; is computationally less expensive and leads to improved energy conservation
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.2
; MARTINI and NONBONDED
; Standard cut-off schemes are used for the non-bonded interactions
; in the Martini model: LJ interactions are shifted to zero in the
; range 0.9-1.2 nm, and electrostatic interactions in the range 0.0-1.2 nm.
; The treatment of the non-bonded cut-offs is considered to be part of
; the force field parameterization, so we recommend not to touch these
; values as they will alter the overall balance of the force field.
; In principle you can include long range electrostatics through the use
; of PME, which could be more realistic in certain applications
; Please realize that electrostatic 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.
;
; For use in combination with the Verlet-pairlist algorithm implemented
; in Gromacs 4.6 a straight cutoff in combination with the potential
; modifiers can be used. Although this will change the potential shape,
; preliminary results indicate that forcefield properties do not change a lot
; when the LJ cutoff is reduced to 1.1 nm. Be sure to test the effects for
; your particular system. The advantage is a gain of speed of 50-100%.
coulombtype = Shift ;Reaction_field (for use with Verlet-pairlist) ;PME (especially with polarizable water)
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15 ; 2.5 (with polarizable water)
vdw_type = Shift ;cutoff (for use with Verlet-pairlist)
rvdw_switch = 0.9
rvdw = 1.2 ;1.1 (for use with Verlet-pairlist)
;cutoff-scheme = verlet
;coulomb-modifier = Potential-shift
;vdw-modifier = Potential-shift
;epsilon_rf = 0 ; epsilon_rf = 0 really means epsilon_rf = infinity
;verlet-buffer-drift = 0.005
; 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 10-4 - 10-5 bar-1. Note that, for equilibration purposes,
; the Berendsen thermostat 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 = DPPC DUPC CHOL W
tau_t = 1.0 1.0 1.0 1.0
ref_t = 295 295 295 295
Pcoupl = Berendsen
Pcoupltype = semiisotropic
tau_p = 4.0 4.0 ;parrinello-rahman is more stable with larger tau-p, DdJ, 20130422
compressibility = 5e-5 5e-5
ref_p = 1.0 1.0
gen_vel = yes
gen_temp = 295
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
unconstrained_start = no
lincs_order = 8 ; changed from 4 to 8 for new chol
lincs_iter = 2 ; added for new chol
lincs_warnangle = 30
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- mic339
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9 years 6 months ago #4117
by mic339
Replied by mic339 on topic GROMACS Version 5
Since in Gromacs v5 the cutoff-scheme is Verlet by default you have to specify that you want to use the deprecated group scheme by including the option
cutoff-scheme = group
in your mdp file, that will remove the errors you are seeing since both are related to the Verlet scheme. I can't comment on whether there are other issues with Gromacs 5 and MARTINI as I haven't tested it yet.
cutoff-scheme = group
in your mdp file, that will remove the errors you are seeing since both are related to the Verlet scheme. I can't comment on whether there are other issues with Gromacs 5 and MARTINI as I haven't tested it yet.
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- kmcg
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9 years 2 months ago #4470
by kmcg
Replied by kmcg on topic GROMACS Version 5
Is there an update for the incorporation of Gromacs 5 and Martini?
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- Sikora
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9 years 20 hours ago #4525
by Sikora
Replied by Sikora on topic GROMACS Version 5
Hi All,
has there been any progress with determining if Verlt scheme with shift potential modifiers would work in Gromacs 5? It is the only version we have on our cluster.
has there been any progress with determining if Verlt scheme with shift potential modifiers would work in Gromacs 5? It is the only version we have on our cluster.
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