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minimum energy of a single DPPC molecule
- panzu
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Topic Author
- Visitor
10 years 11 months ago #1575
by panzu
minimum energy of a single DPPC molecule was created by panzu
Dear all,
I got the next fact,I hope you can help me.
I would like to get the minimum of energy of a single molecule of DPPC.Therefore by adding it in gromacs at very low temperatures what I find is that at very low temperature (20 K ) the molecule is shrunken and at high temperatures(400 K) the molecule is totally frozen, flat and rigid.This is totally the opposite to what I expected.Does anybody know what is going on?
I also attach the parameters.
; VARIOUS PREPROCESSING OPTIONS =
title = Martini
cpp = /usr/bin/cpp
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit = 0.0
dt = 0.040
nsteps = 1000
; number of steps for center of mass motion removal =
nstcomm = 1
comm-grps = DPPC
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 100
nstvout = 100
nstfout = 100
; Output frequency for energies to log file and energy file =
nstlog = 1000
nstenergy = 100
; Output frequency and precision for xtc file =
nstxtcout = 1000
xtc_precision = 10000
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps = DPPC
; Selection of energy groups =
energygrps = DPPC
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist = 10
; ns algorithm (simple or grid) =
ns_type = grid
; Periodic boundary conditions: xyz or none =
pbc = xyz
; nblist cut-off =
rlist = 1.4
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r = 15
; Method for doing Van der Waals =
vdw_type = Shift
; cut-off lengths =
rvdw_switch = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
tcoupl = Berendsen
;tcoupl = V-rescale
; Groups to couple separately =
tc-grps = DPPC
; Time constant (ps) and reference temperature (K) =
tau_t = 1.0
ref_t = 20
; Pressure coupling =
Pcuppl = no
;Pcoupl = berendsen
;Pcoupltype = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 4.5 4.5
compressibility = 3e-5 3e-5
ref_p = 1.0 1.0
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = no
gen_temp = 300
gen_seed = -1
; OPTIONS FOR BONDS =
constraints = none
; Type of constraint algorithm =
constraint_algorithm = Lincs
; Do not constrain the start configuration =
unconstrained_start = no
; Highest order in the expansion of the constraint coupling matrix =
lincs_order = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs_warnangle = 30
I got the next fact,I hope you can help me.
I would like to get the minimum of energy of a single molecule of DPPC.Therefore by adding it in gromacs at very low temperatures what I find is that at very low temperature (20 K ) the molecule is shrunken and at high temperatures(400 K) the molecule is totally frozen, flat and rigid.This is totally the opposite to what I expected.Does anybody know what is going on?
I also attach the parameters.
; VARIOUS PREPROCESSING OPTIONS =
title = Martini
cpp = /usr/bin/cpp
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit = 0.0
dt = 0.040
nsteps = 1000
; number of steps for center of mass motion removal =
nstcomm = 1
comm-grps = DPPC
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 100
nstvout = 100
nstfout = 100
; Output frequency for energies to log file and energy file =
nstlog = 1000
nstenergy = 100
; Output frequency and precision for xtc file =
nstxtcout = 1000
xtc_precision = 10000
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps = DPPC
; Selection of energy groups =
energygrps = DPPC
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist = 10
; ns algorithm (simple or grid) =
ns_type = grid
; Periodic boundary conditions: xyz or none =
pbc = xyz
; nblist cut-off =
rlist = 1.4
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r = 15
; Method for doing Van der Waals =
vdw_type = Shift
; cut-off lengths =
rvdw_switch = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
tcoupl = Berendsen
;tcoupl = V-rescale
; Groups to couple separately =
tc-grps = DPPC
; Time constant (ps) and reference temperature (K) =
tau_t = 1.0
ref_t = 20
; Pressure coupling =
Pcuppl = no
;Pcoupl = berendsen
;Pcoupltype = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 4.5 4.5
compressibility = 3e-5 3e-5
ref_p = 1.0 1.0
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = no
gen_temp = 300
gen_seed = -1
; OPTIONS FOR BONDS =
constraints = none
; Type of constraint algorithm =
constraint_algorithm = Lincs
; Do not constrain the start configuration =
unconstrained_start = no
; Highest order in the expansion of the constraint coupling matrix =
lincs_order = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs_warnangle = 30
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- xavier
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- Offline
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10 years 11 months ago #1582
by xavier
Replied by xavier on topic minimum energy of a single DPPC molecule
In vacuo you need to switch to the sd integrator to be able to have a reasonable temperature of your system ...
panzu wrote: Dear all,
I got the next fact,I hope you can help me.
I would like to get the minimum of energy of a single molecule of DPPC.Therefore by adding it in gromacs at very low temperatures what I find is that at very low temperature (20 K ) the molecule is shrunken and at high temperatures(400 K) the molecule is totally frozen, flat and rigid.This is totally the opposite to what I expected.Does anybody know what is going on?
I also attach the parameters.
; VARIOUS PREPROCESSING OPTIONS =
title = Martini
cpp = /usr/bin/cpp
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit = 0.0
dt = 0.040
nsteps = 1000
; number of steps for center of mass motion removal =
nstcomm = 1
comm-grps = DPPC
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 100
nstvout = 100
nstfout = 100
; Output frequency for energies to log file and energy file =
nstlog = 1000
nstenergy = 100
; Output frequency and precision for xtc file =
nstxtcout = 1000
xtc_precision = 10000
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps = DPPC
; Selection of energy groups =
energygrps = DPPC
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist = 10
; ns algorithm (simple or grid) =
ns_type = grid
; Periodic boundary conditions: xyz or none =
pbc = xyz
; nblist cut-off =
rlist = 1.4
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r = 15
; Method for doing Van der Waals =
vdw_type = Shift
; cut-off lengths =
rvdw_switch = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
tcoupl = Berendsen
;tcoupl = V-rescale
; Groups to couple separately =
tc-grps = DPPC
; Time constant (ps) and reference temperature (K) =
tau_t = 1.0
ref_t = 20
; Pressure coupling =
Pcuppl = no
;Pcoupl = berendsen
;Pcoupltype = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 4.5 4.5
compressibility = 3e-5 3e-5
ref_p = 1.0 1.0
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = no
gen_temp = 300
gen_seed = -1
; OPTIONS FOR BONDS =
constraints = none
; Type of constraint algorithm =
constraint_algorithm = Lincs
; Do not constrain the start configuration =
unconstrained_start = no
; Highest order in the expansion of the constraint coupling matrix =
lincs_order = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs_warnangle = 30
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