[gmx-users] [Fwd: Problems in pulling a molecule from the membrane]
Berk Hess
gmx3 at hotmail.com
Fri Mar 27 15:13:44 CET 2009
Hi,
First let me say you should change to 4.0.4.
I don't recall if there would be problems with your setup, but 4.0.4 has many bugfixes.
I guess you problem is that you use pull_start and pull_init togther,
which I guess produces double the effect you want.
Please read the mdp manual.
I guess you should use only one of the two options.
Berk
Date: Fri, 27 Mar 2009 14:43:48 +0100
From: schlesi at uni-mainz.de
To: gmx-users at gromacs.org
Subject: [gmx-users] [Fwd: Problems in pulling a molecule from the membrane]
I have tested the pulling in GROMACS 4.0.2 only once and there only with
'pull_geometry = position'. But i think the problem lies in the
pressure-coupling or something which is connected to it ' Step 1
Warning: pressure scaling more than 1%, mu: 1.00054 1.00054 0.83511'.
Because i have not yet used pressure-coupling (only done NVT) . So the
only think i can do is:
Look at:
http://wiki.gromacs.org/index.php/Errors#Pressure_scaling_more_than_1.25
Sorry that i can not give more help.
Probably one thing:
I would try 'tinit=0'. I do not know how the code works, but i can
imagine that with a non-zero value, the spring move but the system
cannot do something. Then when the real simulation begins the spring has
actually moved and you have an force acting on your pull-group which is
much higher then with 'tinit=0'. But this is only an idea and i do not
know if it has any relevance . Probalby one of the other guys knows if
this matters.
Thomas
========================================================
Dear Thomas,
I found your name from the gromacs mailing list. As you are the
one of the fortunate persons who has able to do pulling in gromacs 4.02,
I directly mail you. I want to pull a molecule from the membrane. My
complete mdp file is the following
;.............................
............................................................................................................................................................................
; File 'mdout.mdp' was generated
; By user: psn (17109)
; On host: p690k
; At date: Fri Jul 23 12:43:31 2004
;
; VARIOUS PREPROCESSING OPTIONS =
title = lipid bilayer in water
cpp = /lib/cpp
include =
define =
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit = 500
dt = 0.002
nsteps = 1750000
; mode for center of mass motion removal =
comm-mode = Linear
; number of steps for center of mass motion removal =
nstcomm = 1
; group(s) for center of mass motion removal =
comm-grps =
; LANGEVIN DYNAMICS OPTIONS =
; Temperature, friction coefficient (amu/ps) and random seed =
;bd-temp = 300
;I have commute the above line as it has no exitance
bd-fric = 0
ld-seed = 1993
; ENERGY MINIMIZATION OPTIONS =
; Force tolerance and initial step-size =
emtol = 100
emstep = 0.01
; Max number of iterations in relax_shells =
niter = 20
; Step size (1/ps^2) for minimization of flexible constraints =
fcstep = 0
; Frequency of steepest descents steps when doing CG =
nstcgsteep = 1000
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 5000
nstvout = 5000
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 250
nstenergy = 250
; Output frequency and precision for xtc file =
nstxtcout = 0
xtc-precision = 1000
; 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 =
; nblist update frequency =
nstlist = 10
; ns algorithm (simple or grid) =
ns_type = grid
; Periodic boundary conditions: xyz or no =
pbc = xyz
; nblist cut-off =
rlist = 1.0
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype = PME ;Reaction-Field
rcoulomb-switch = 0
rcoulomb = 1.0 ;2.0
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r = 80.0
epsilon_rf = 1
;I have done some thing new according to mannual and warnings and error
; Method for doing Van der Waals =
vdwtype = Cut-off
; cut-off lengths =
rvdw-switch = 0
rvdw = 1.0
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; Spacing for the PME/PPPM FFT grid =
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters =
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = yes
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
Tcoupl = berendsen
; Groups to couple separately =
tc-grps = DPP SOL Na PIP
; Time constant (ps) and reference temperature (K) =
tau_t = 0.1 0.1 0.1 0.1
ref_t = 310 310 310 310
; Pressure coupling =
Pcoupl = berendsen
Pcoupltype = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 1.0 1.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
; SIMULATED ANNEALING CONTROL =
annealing = no
; Time at which temperature should be zero (ps) =
;zero-temp_time = 0
;I have commute the above line as it has no exitance
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = yes
gen_temp = 310.0
gen_seed = 173529
; OPTIONS FOR BONDS =
constraints = all-bonds
; Type of constraint algorithm =
constraint_algorithm = lincs
; Do not constrain the start configuration =
unconstrained-start = no
; Use successive overrelaxation to reduce the number of shake iterations =
Shake-SOR = no
; Relative tolerance of shake =
shake-tol = 0.0001
; 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
; Convert harmonic bonds to morse potentials =
morse = no
; ENERGY GROUP EXCLUSIONS =
; Pairs of energy groups for which all non-bonded interactions are
excluded =
energygrp_excl =
;............................................................................................................
;pulling
pull = umbrella
pull_geometry = direction
pull_start = yes
pull_ngroups = 1
pull_group0 = DPP
pull_group1 = PIP
pull_dim = N N Y
pull_k1 = 500
pull_kB1 = 500
pull_rate1 = 0.005
pull_vec1 = 0 0 -1
pull_init1 = -1.822
pull_nstxout = 100
; NMR refinement stuff =
; Distance restraints type: No, Simple or Ensemble =
disre = No
; Force weighting of pairs in one distance restraint: Conservative or
Equal =
disre-weighting = Conservative
; Use sqrt of the time averaged times the instantaneous violation =
disre-mixed = no
disre-fc = 1000
disre-tau = 0
; Output frequency for pair distances to energy file =
nstdisreout = 100
; Orientation restraints: No or Yes =
orire = no
; Orientation restraints force constant and tau for time averaging =
orire-fc = 0
orire-tau = 0
orire-fitgrp =
; Output frequency for trace(SD) to energy file =
nstorireout = 100
; Free energy control stuff =
free-energy = no
init-lambda = 0
delta-lambda = 0
sc-alpha = 0
sc-sigma = 0.3
; Non-equilibrium MD stuff =
acc-grps =
accelerate =
freezegrps =
freezedim =
cos-acceleration = 0
; Electric fields =
; Format is number of terms (int) and for all terms an amplitude (real) =
; and a phase angle (real) =
E-x =
E-xt =
E-y =
E-yt =
E-z =
E-zt =
; User defined thingies =
user1-grps =
user2-grps =
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
..............................................................................................................................................................................................................................................................
Here, in the first step, there is no error or warning during the making
of .tpr file. But in the mdrun, after 3/4 steps, it crashes ans stop
the MD run. It gives the following error message:
Back Off! I just backed up dppc_pip2-ion_NPT_berendsen_md.edr
to ./#dppc_pip2-ion_NPT_berendsen_md.edr.2#
starting mdrun 'Pure 122 DPPC and 1 PIP2 molecule bilayer with 3592
water molecules'
1750000 steps, 3500.0 ps.
step 0
Step 1 Warning: pressure scaling more than 1%, mu: 1.00054 1.00054 0.83511
Step 1 Warning: pressure scaling more than 1%, mu: 1.00054 1.00054 0.83511
Step 1 Warning: pressure scaling more than 1%, mu: 1.00054 1.00054 0.83511
.............................................
t = 500.004 ps: Water molecule starting at atom 10595 can not be settled.
Check for bad contacts and/or reduce the timestep.
Step 2, time 500.004 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 35.655980, max 638.714233 (between atoms 2849 and 2848)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
943 942 54.9 0.1498 3.0441 0.1530
942 941 88.6 0.1297 0.2327 0.1530
943 944 93.1 0.1291 20.4158 0.1530
944 945 93.6 0.1491 116.4443 0.1530
................................
Wrote pdb files with previous and current coordinates
-----------------------------------------------------------------------------
One of the processes started by mpirun has exited with a nonzero exit
code. This typically indicates that the process finished in error.
If your process did not finish in error, be sure to include a "return
0" or "exit(0)" in your C code before exiting the application.
PID 21625 failed on node n0 (127.0.0.1) due to signal 11.
-----------------------------------------------------------------------------
/opt/torque/mom_priv/jobs/692.srclust.SC <http://692.srclust.sc/>: line
20: unexpected EOF while looking for matching `''
/opt/torque/mom_priv/jobs/692.srclust.SC <http://692.srclust.sc/>: line
21: syntax error: unexpected end of file
Could you please tell me where I have done mistake. In
my system, the PIP molecule (pulled molecule) is situated at the bottom
layer (from -z direction). So, I wrote
pull_vec1 = 0 0 -1
Could you please help me?
Thanking you,
Anirban
--Forwarded Message Attachment--
From: polley.anirban at gmail.com
To: schlesi at uni-mainz.de
Date: Fri, 27 Mar 2009 07:13:51 +0100
Subject: Problems in pulling a molecule from the membrane
Dear Thomas,
I found your name from the gromacs
mailing list. As you are the one of the fortunate persons who has able
to do pulling in gromacs 4.02, I directly mail you. I want to
pull a molecule from the membrane. My complete mdp file is the following
;.............................
............................................................................................................................................................................
; File 'mdout.mdp' was generated
; By user: psn (17109)
; On host: p690k
; At date: Fri Jul 23 12:43:31 2004
;
; VARIOUS PREPROCESSING OPTIONS =
title
= lipid bilayer in water
cpp
= /lib/cpp
include =
define =
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit = 500
dt
= 0.002
nsteps = 1750000
; mode for center of mass motion removal =
comm-mode = Linear
; number of steps for center of mass motion removal =
nstcomm = 1
; group(s) for center of mass motion removal =
comm-grps =
; LANGEVIN DYNAMICS OPTIONS =
; Temperature, friction coefficient (amu/ps) and random seed =
;bd-temp = 300
;I have commute the above line as it has no exitance
bd-fric = 0
ld-seed = 1993
; ENERGY MINIMIZATION OPTIONS =
; Force tolerance and initial step-size =
emtol = 100
emstep = 0.01
; Max number of iterations in relax_shells =
niter = 20
; Step size (1/ps^2) for minimization of flexible constraints =
fcstep = 0
; Frequency of steepest descents steps when doing CG =
nstcgsteep = 1000
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 5000
nstvout = 5000
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 250
nstenergy = 250
; Output frequency and precision for xtc file =
nstxtcout = 0
xtc-precision = 1000
; 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 =
; nblist update frequency =
nstlist = 10
; ns algorithm (simple or grid) =
ns_type = grid
; Periodic boundary conditions: xyz or no =
pbc
= xyz
; nblist cut-off =
rlist = 1.0
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype
= PME ;Reaction-Field
rcoulomb-switch = 0
rcoulomb
= 1.0 ;2.0
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r = 80.0
epsilon_rf = 1
;I have done some thing new according to mannual and warnings and error
; Method for doing Van der Waals =
vdwtype = Cut-off
; cut-off lengths =
rvdw-switch = 0
rvdw
= 1.0
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; Spacing for the PME/PPPM FFT grid =
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters =
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = yes
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
Tcoupl = berendsen
; Groups to couple separately =
tc-grps
= DPP SOL Na PIP
; Time constant (ps) and reference temperature (K) =
tau_t
= 0.1 0.1 0.1 0.1
ref_t
= 310 310 310 310
; Pressure coupling =
Pcoupl = berendsen
Pcoupltype = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p
= 1.0 1.0
compressibility = 4.5e-5 4.5e-5
ref_p
= 1.0 1.0
; SIMULATED ANNEALING CONTROL =
annealing = no
; Time at which temperature should be zero (ps) =
;zero-temp_time = 0
;I have commute the above line as it has no exitance
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = yes
gen_temp = 310.0
gen_seed = 173529
; OPTIONS FOR BONDS =
constraints = all-bonds
; Type of constraint algorithm =
constraint_algorithm = lincs
; Do not constrain the start configuration =
unconstrained-start = no
; Use successive overrelaxation to reduce the number of shake iterations =
Shake-SOR = no
; Relative tolerance of shake =
shake-tol = 0.0001
; 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
; Convert harmonic bonds to morse potentials =
morse = no
; ENERGY GROUP EXCLUSIONS =
; Pairs of energy groups for which all non-bonded interactions are excluded =
energygrp_excl =
;............................................................................................................
;pulling
pull = umbrella
pull_geometry = direction
pull_start = yes
pull_ngroups = 1
pull_group0 = DPP
pull_group1 = PIP
pull_dim = N N Y
pull_k1 = 500
pull_kB1 = 500
pull_rate1 = 0.005
pull_vec1 = 0 0 -1
pull_init1 = -1.822
pull_nstxout = 100
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