[gmx-users] Asymmetric potential for 512 dppc bilayer using martini
Adwait Mevada
adwait at imsc.res.in
Mon Aug 10 15:14:28 CEST 2009
Dear gmx-users,
I downloaded gro file containing 128 dppc lipids and 2000 waters from,
Marrink's website, extracted the lipids and replicated using genconf,
after minimization I added 2700 waters to it, minimized the system.
Then gave an mdrun for 27ns. I did an potential analysis which results
in an asymmetric bilayer profile. Can you tell me as to why am i
getting such a result? I am
using Martini force field 2.0 and gromacs version 3.3.3.
I am attaching my mdp files and the potential results.
##### em.mdp ######
;
; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0
;
; for use with GROMACS 3.3
;
; VARIOUS PREPROCESSING OPTIONS =
title = Martini
cpp = /usr/bin/cpp
; RUN CONTROL PARAMETERS =
; MARTINI - Most simulations are stable with dt=40 fs,
; some (especially rings) require 20-30 fs.
; The range of time steps used for parametrization
; is 20-40 fs, using smaller time steps is therefore not recommended.
integrator = steep
; start time and timestep in ps
tinit = 0.0
dt = 0.030
nsteps = 100000
; number of steps for center of mass motion removal =
nstcomm = 1
comm-grps =
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstvout = 2500
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 1000
nstenergy = 1000
; Output frequency and precision for xtc file =
nstxtcout = 1000
xtc_precision = 100
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps =
; Selection of energy groups =
energygrps =
; NEIGHBORSEARCHING PARAMETERS =
; MARTINI - no need for more frequent updates
; or larger neighborlist cut-off due
; to the use of shifted potential energy functions.
; 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 = 1.3
; OPTIONS FOR ELECTROSTATICS AND VDW =
; MARTINI - vdw and electrostatic interactions are used
; in their shifted forms. Changing to other types of
; electrostatics will affect the general performance of
; the model.
; 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 =
; MARTINI - normal temperature and pressure coupling schemes
; can be used. It is recommended to couple individual groups
; in your system seperately.
; Temperature coupling =
tcoupl = no
; Groups to couple separately =
tc-grps = DPPC
; Time constant (ps) and reference temperature (K) =
tau_t = 0.3
ref_t = 323
; Pressure coupling =
Pcoupl = no
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 3.0
compressibility = 3e-5
ref_p = 1.0
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = no
gen_temp = 323
gen_seed = 666
; OPTIONS FOR BONDS =
; MARTINI - for ring systems constraints are defined
; which are best handled using Lincs.
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
##### md.mdp #####
;
; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0
;
; for use with GROMACS 3.3
;
; VARIOUS PREPROCESSING OPTIONS =
title = Martini
cpp = /usr/bin/cpp
; RUN CONTROL PARAMETERS =
; MARTINI - Most simulations are stable with dt=40 fs,
; some (especially rings) require 20-30 fs.
; The range of time steps used for parametrization
; is 20-40 fs, using smaller time steps is therefore not recommended.
integrator = md
; start time and timestep in ps
tinit = 0.0
dt = 0.030
nsteps = 900000
; number of steps for center of mass motion removal =
nstcomm = 1
comm-grps =
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstvout = 2500
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 1000
nstenergy = 1000
; Output frequency and precision for xtc file =
nstxtcout = 1000
xtc_precision = 100
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps =
; Selection of energy groups =
energygrps =
; NEIGHBORSEARCHING PARAMETERS =
; MARTINI - no need for more frequent updates
; or larger neighborlist cut-off due
; to the use of shifted potential energy functions.
; 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 = 1.3
; OPTIONS FOR ELECTROSTATICS AND VDW =
; MARTINI - vdw and electrostatic interactions are used
; in their shifted forms. Changing to other types of
; electrostatics will affect the general performance of
; the model.
; 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 =
; MARTINI - normal temperature and pressure coupling schemes
; can be used. It is recommended to couple individual groups
; in your system seperately.
; Temperature coupling =
tcoupl = Berendsen
; Groups to couple separately =
tc-grps = DPPC W
; Time constant (ps) and reference temperature (K) =
tau_t = 0.3 0.3
ref_t = 323 323
; Pressure coupling =
Pcoupl = berendsen
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 3.0
compressibility = 3e-5
ref_p = 1.0
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = no
gen_temp = 323
gen_seed = 666
; OPTIONS FOR BONDS =
; MARTINI - for ring systems constraints are defined
; which are best handled using Lincs.
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
###### potential.xvg #########
# This file was created Thu Jul 23 16:04:17 2009
# by the following command:
# g_potential -f dppc_w_md.trr -s dppc_w_md.tpr -sl 100
#
# g_potential is part of G R O M A C S:
#
# Good ROcking Metal Altar for Chronical Sinners
#
@ title "Electrostatic Potential"
@ xaxis label "Box (nm)"
@ yaxis label "Potential (V)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "System"
0 -0
0.054134 -0.00608947
0.108268 -0.0259436
0.162402 -0.0628989
0.216536 -0.119664
0.27067 -0.19744
0.324804 -0.296039
0.378938 -0.414183
0.433072 -0.550079
0.487206 -0.701776
0.54134 -0.866225
0.595474 -1.03589
0.649608 -1.2001
0.703742 -1.34992
0.757876 -1.48031
0.81201 -1.58991
0.866144 -1.67761
0.920278 -1.74336
0.974412 -1.78992
1.02855 -1.82017
1.08268 -1.83703
1.13681 -1.84384
1.19095 -1.84274
1.24508 -1.83573
1.29922 -1.8255
1.35335 -1.81335
1.40748 -1.79979
1.46162 -1.78536
1.51575 -1.77046
1.56989 -1.75528
1.62402 -1.73976
1.67815 -1.72404
1.73229 -1.70819
1.78642 -1.69219
1.84056 -1.67609
1.89469 -1.65982
1.94882 -1.6433
2.00296 -1.62675
2.05709 -1.61004
2.11123 -1.59284
2.16536 -1.5752
2.21949 -1.55709
2.27363 -1.5385
2.32776 -1.5196
2.3819 -1.50031
2.43603 -1.48069
2.49016 -1.46086
2.5443 -1.44087
2.59843 -1.42081
2.65257 -1.40055
2.7067 -1.38003
2.76083 -1.35938
2.81497 -1.33868
2.8691 -1.31795
2.92324 -1.29698
2.97737 -1.27553
3.0315 -1.25374
3.08564 -1.23182
3.13977 -1.20987
3.19391 -1.18777
3.24804 -1.16527
3.30217 -1.14239
3.35631 -1.11961
3.41044 -1.09729
3.46458 -1.07488
3.51871 -1.05166
3.57284 -1.02764
3.62698 -1.00328
3.68111 -0.978466
3.73525 -0.952391
3.78938 -0.9243
3.84351 -0.893929
3.89765 -0.861214
3.95178 -0.825899
4.00592 -0.786147
4.06005 -0.739105
4.11418 -0.682758
4.16832 -0.614639
4.22245 -0.532118
4.27659 -0.433156
4.33072 -0.313756
4.38485 -0.169271
4.43899 -0.000186288
4.49312 0.188136
4.54726 0.389892
4.60139 0.598806
4.65553 0.807787
4.70966 1.00958
4.76379 1.19832
4.81793 1.36919
4.87206 1.51743
4.9262 1.64199
4.98033 1.74516
5.03446 1.82958
5.0886 1.89744
5.14273 1.95057
5.19687 1.99145
5.251 2.02238
5.30513 2.04472
5.35927 2.05877
-Adwait
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