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Hi,<br><br>First let me say you should change to 4.0.4.<br>I don't recall if there would be problems with your setup, but 4.0.4 has many bugfixes.<br><br>I guess you problem is that you use pull_start and pull_init togther,<br>which I guess produces double the effect you want.<br>Please read the mdp manual.<br>I guess you should use only one of the two options.<br><br>Berk<br><br>Date: Fri, 27 Mar 2009 14:43:48 +0100<br>From: schlesi@uni-mainz.de<br>To: gmx-users@gromacs.org<br>Subject: [gmx-users] [Fwd: Problems in pulling a molecule from the membrane]<br><br><pre>I have tested the pulling in GROMACS 4.0.2 only once and there only with<br>'pull_geometry = position'. But i think the problem lies in the<br>pressure-coupling or something which is connected to it ' Step 1 <br>Warning: pressure scaling more than 1%, mu: 1.00054 1.00054 0.83511'.<br>Because i have not yet used pressure-coupling (only done NVT) . So the<br>only think i can do is:<br>Look at:<br><a href="http://wiki.gromacs.org/index.php/Errors#Pressure_scaling_more_than_1.25">http://wiki.gromacs.org/index.php/Errors#Pressure_scaling_more_than_1.25</a><br>Sorry that i can not give more help.<br> <br>Probably one thing:<br>I would try 'tinit=0'. I do not know how the code works, but i can<br>imagine that with a non-zero value, the spring move but the system<br>cannot do something. Then when the real simulation begins the spring has<br>actually moved and you have an force acting on your pull-group which is<br>much higher then with 'tinit=0'. But this is only an idea and i do not<br>know if it has any relevance . Probalby one of the other guys knows if<br>this matters.<br> <br>Thomas<br> <br>========================================================<br> <br>Dear Thomas,<br> I found your name from the gromacs mailing list. As you are the<br>one of the fortunate persons who has able to do pulling in gromacs 4.02,<br>I directly mail you. I want to pull a molecule from the membrane. My<br>complete mdp file is the following<br>;.............................<br>............................................................................................................................................................................<br>; File 'mdout.mdp' was generated<br>; By user: psn (17109)<br>; On host: p690k<br>; At date: Fri Jul 23 12:43:31 2004<br>;<br> <br>; VARIOUS PREPROCESSING OPTIONS =<br>title = lipid bilayer in water<br>cpp = /lib/cpp<br>include =<br>define =<br> <br>; RUN CONTROL PARAMETERS =<br>integrator = md<br>; start time and timestep in ps =<br>tinit = 500<br>dt = 0.002<br>nsteps = 1750000<br>; mode for center of mass motion removal =<br>comm-mode = Linear<br>; number of steps for center of mass motion removal =<br>nstcomm = 1<br>; group(s) for center of mass motion removal =<br>comm-grps =<br> <br>; LANGEVIN DYNAMICS OPTIONS =<br>; Temperature, friction coefficient (amu/ps) and random seed =<br>;bd-temp = 300<br>;I have commute the above line as it has no exitance<br>bd-fric = 0<br>ld-seed = 1993<br> <br>; ENERGY MINIMIZATION OPTIONS =<br>; Force tolerance and initial step-size =<br>emtol = 100<br>emstep = 0.01<br>; Max number of iterations in relax_shells =<br>niter = 20<br>; Step size (1/ps^2) for minimization of flexible constraints =<br>fcstep = 0<br>; Frequency of steepest descents steps when doing CG =<br>nstcgsteep = 1000<br> <br>; OUTPUT CONTROL OPTIONS =<br>; Output frequency for coords (x), velocities (v) and forces (f) =<br>nstxout = 5000<br>nstvout = 5000<br>nstfout = 0<br>; Output frequency for energies to log file and energy file =<br>nstlog = 250<br>nstenergy = 250<br>; Output frequency and precision for xtc file =<br>nstxtcout = 0<br>xtc-precision = 1000<br>; This selects the subset of atoms for the xtc file. You can =<br>; select multiple groups. By default all atoms will be written. =<br>xtc-grps =<br>; Selection of energy groups =<br>energygrps =<br> <br>; NEIGHBORSEARCHING PARAMETERS =<br>; nblist update frequency =<br>nstlist = 10<br>; ns algorithm (simple or grid) =<br>ns_type = grid<br>; Periodic boundary conditions: xyz or no =<br>pbc = xyz<br>; nblist cut-off =<br>rlist = 1.0<br>domain-decomposition = no<br> <br>; OPTIONS FOR ELECTROSTATICS AND VDW =<br>; Method for doing electrostatics =<br>coulombtype = PME ;Reaction-Field<br>rcoulomb-switch = 0<br>rcoulomb = 1.0 ;2.0<br>; Dielectric constant (DC) for cut-off or DC of reaction field =<br>epsilon_r = 80.0<br>epsilon_rf = 1<br>;I have done some thing new according to mannual and warnings and error<br>; Method for doing Van der Waals =<br>vdwtype = Cut-off<br>; cut-off lengths =<br>rvdw-switch = 0<br>rvdw = 1.0<br>; Apply long range dispersion corrections for Energy and Pressure =<br>DispCorr = No<br>; Spacing for the PME/PPPM FFT grid =<br>fourierspacing = 0.12<br>; FFT grid size, when a value is 0 fourierspacing will be used =<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>; EWALD/PME/PPPM parameters =<br>pme_order = 4<br>ewald_rtol = 1e-05<br>ewald_geometry = 3d<br>epsilon_surface = 0<br>optimize_fft = yes<br> <br>; OPTIONS FOR WEAK COUPLING ALGORITHMS =<br>; Temperature coupling =<br>Tcoupl = berendsen<br>; Groups to couple separately =<br>tc-grps = DPP SOL Na PIP<br>; Time constant (ps) and reference temperature (K) =<br>tau_t = 0.1 0.1 0.1 0.1<br>ref_t = 310 310 310 310<br>; Pressure coupling =<br>Pcoupl = berendsen<br>Pcoupltype = semiisotropic<br>; Time constant (ps), compressibility (1/bar) and reference P (bar) =<br>tau_p = 1.0 1.0<br>compressibility = 4.5e-5 4.5e-5<br>ref_p = 1.0 1.0<br> <br>; SIMULATED ANNEALING CONTROL =<br>annealing = no<br>; Time at which temperature should be zero (ps) =<br>;zero-temp_time = 0<br>;I have commute the above line as it has no exitance<br> <br>; GENERATE VELOCITIES FOR STARTUP RUN =<br>gen_vel = yes<br>gen_temp = 310.0<br>gen_seed = 173529<br> <br>; OPTIONS FOR BONDS =<br>constraints = all-bonds<br>; Type of constraint algorithm =<br>constraint_algorithm = lincs<br>; Do not constrain the start configuration =<br>unconstrained-start = no<br>; Use successive overrelaxation to reduce the number of shake iterations =<br>Shake-SOR = no<br>; Relative tolerance of shake =<br>shake-tol = 0.0001<br>; Highest order in the expansion of the constraint coupling matrix =<br>lincs_order = 4<br>; Lincs will write a warning to the stderr if in one step a bond =<br>; rotates over more degrees than =<br>lincs-warnangle = 30<br>; Convert harmonic bonds to morse potentials =<br>morse = no<br> <br>; ENERGY GROUP EXCLUSIONS =<br>; Pairs of energy groups for which all non-bonded interactions are<br>excluded =<br>energygrp_excl =<br> <br>;............................................................................................................<br>;pulling<br>pull = umbrella<br>pull_geometry = direction<br>pull_start = yes<br>pull_ngroups = 1<br>pull_group0 = DPP<br>pull_group1 = PIP<br>pull_dim = N N Y<br>pull_k1 = 500<br>pull_kB1 = 500<br>pull_rate1 = 0.005<br>pull_vec1 = 0 0 -1<br>pull_init1 = -1.822<br>pull_nstxout = 100<br> <br>; NMR refinement stuff =<br>; Distance restraints type: No, Simple or Ensemble =<br>disre = No<br>; Force weighting of pairs in one distance restraint: Conservative or<br>Equal =<br>disre-weighting = Conservative<br>; Use sqrt of the time averaged times the instantaneous violation =<br>disre-mixed = no<br>disre-fc = 1000<br>disre-tau = 0<br>; Output frequency for pair distances to energy file =<br>nstdisreout = 100<br>; Orientation restraints: No or Yes =<br>orire = no<br>; Orientation restraints force constant and tau for time averaging =<br>orire-fc = 0<br>orire-tau = 0<br>orire-fitgrp =<br>; Output frequency for trace(SD) to energy file =<br>nstorireout = 100<br> <br>; Free energy control stuff =<br>free-energy = no<br>init-lambda = 0<br>delta-lambda = 0<br>sc-alpha = 0<br>sc-sigma = 0.3<br> <br>; Non-equilibrium MD stuff =<br>acc-grps =<br>accelerate =<br>freezegrps =<br>freezedim =<br>cos-acceleration = 0<br> <br>; Electric fields =<br>; Format is number of terms (int) and for all terms an amplitude (real) =<br>; and a phase angle (real) =<br>E-x =<br>E-xt =<br>E-y =<br>E-yt =<br>E-z =<br>E-zt =<br> <br>; User defined thingies =<br>user1-grps =<br>user2-grps =<br>userint1 = 0<br>userint2 = 0<br>userint3 = 0<br>userint4 = 0<br>userreal1 = 0<br>userreal2 = 0<br>userreal3 = 0<br>..............................................................................................................................................................................................................................................................<br> <br> <br>Here, in the first step, there is no error or warning during the making<br>of .tpr file. But in the mdrun, after 3/4 steps, it crashes ans stop<br>the MD run. It gives the following error message:<br> Back Off! I just backed up dppc_pip2-ion_NPT_berendsen_md.edr<br>to ./#dppc_pip2-ion_NPT_berendsen_md.edr.2#<br>starting mdrun 'Pure 122 DPPC and 1 PIP2 molecule bilayer with 3592<br>water molecules'<br>1750000 steps, 3500.0 ps.<br>step 0<br> <br>Step 1 Warning: pressure scaling more than 1%, mu: 1.00054 1.00054 0.83511<br> <br>Step 1 Warning: pressure scaling more than 1%, mu: 1.00054 1.00054 0.83511<br> <br>Step 1 Warning: pressure scaling more than 1%, mu: 1.00054 1.00054 0.83511<br>.............................................<br> <br>t = 500.004 ps: Water molecule starting at atom 10595 can not be settled.<br>Check for bad contacts and/or reduce the timestep.<br> <br>Step 2, time 500.004 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 35.655980, max 638.714233 (between atoms 2849 and 2848)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 943 942 54.9 0.1498 3.0441 0.1530<br> 942 941 88.6 0.1297 0.2327 0.1530<br> 943 944 93.1 0.1291 20.4158 0.1530<br> 944 945 93.6 0.1491 116.4443 0.1530<br>................................<br> Wrote pdb files with previous and current coordinates<br>-----------------------------------------------------------------------------<br>One of the processes started by mpirun has exited with a nonzero exit<br>code. This typically indicates that the process finished in error.<br>If your process did not finish in error, be sure to include a "return<br>0" or "exit(0)" in your C code before exiting the application.<br> <br>PID 21625 failed on node n0 (127.0.0.1) due to signal 11.<br>-----------------------------------------------------------------------------<br>/opt/torque/mom_priv/jobs/692.srclust.SC <<a href="http://692.srclust.sc/">http://692.srclust.sc/</a>>: line<br>20: unexpected EOF while looking for matching `''<br>/opt/torque/mom_priv/jobs/692.srclust.SC <<a href="http://692.srclust.sc/">http://692.srclust.sc/</a>>: line<br>21: syntax error: unexpected end of file<br> <br> <br> Could you please tell me where I have done mistake. In<br>my system, the PIP molecule (pulled molecule) is situated at the bottom<br>layer (from -z direction). So, I wrote<br> pull_vec1 = 0 0 -1<br> Could you please help me?<br>Thanking you,<br>Anirban<br></pre><br><br>--Forwarded Message Attachment--<br>From: polley.anirban@gmail.com<br>To: schlesi@uni-mainz.de<br>Date: Fri, 27 Mar 2009 07:13:51 +0100<br>Subject: Problems in pulling a molecule from the membrane<br><br>Dear Thomas,<br>
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<br>
;.............................
<div id="EC_mb_0">............................................................................................................................................................................<br>
; File 'mdout.mdp' was generated<br>
; By user: psn (17109)<br>
; On host: p690k<br>
; At date: Fri Jul 23 12:43:31 2004<br>
;<br>
<br>
; VARIOUS PREPROCESSING OPTIONS =<br>
title
= lipid bilayer in water<br>cpp
= /lib/cpp<br>
include =<br>
define =<br>
<br>
; RUN CONTROL PARAMETERS =<br>
integrator = md<br>
; start time and timestep in ps =<br>
tinit = 500<br>
dt
= 0.002<br>
nsteps = 1750000<br>
; mode for center of mass motion removal =<br>
comm-mode = Linear<br>
; number of steps for center of mass motion removal =<br>
nstcomm = 1<br>
; group(s) for center of mass motion removal =<br>
comm-grps =<br>
<br>
; LANGEVIN DYNAMICS OPTIONS =<br>
; Temperature, friction coefficient (amu/ps) and random seed =<br>
;bd-temp = 300<br>
;I have commute the above line as it has no exitance<br>
bd-fric = 0<br>
ld-seed = 1993<br>
<br>
; ENERGY MINIMIZATION OPTIONS =<br>
; Force tolerance and initial step-size =<br>
emtol = 100<br>
emstep = 0.01<br>
; Max number of iterations in relax_shells =<br>
niter = 20<br>
; Step size (1/ps^2) for minimization of flexible constraints =<br>
fcstep = 0<br>
; Frequency of steepest descents steps when doing CG =<br>
nstcgsteep = 1000<br>
<br>
; OUTPUT CONTROL OPTIONS =<br>
; Output frequency for coords (x), velocities (v) and forces (f) =<br>
nstxout = 5000<br>
nstvout = 5000<br>
nstfout = 0<br>
; Output frequency for energies to log file and energy file =<br>
nstlog = 250<br>
nstenergy = 250<br>
; Output frequency and precision for xtc file =<br>
nstxtcout = 0<br>
xtc-precision = 1000<br>
; This selects the subset of atoms for the xtc file. You can =<br>
; select multiple groups. By default all atoms will be written. =<br>
xtc-grps =<br>
; Selection of energy groups =<br>
energygrps =<br>
<br>
; NEIGHBORSEARCHING PARAMETERS =<br>
; nblist update frequency =<br>
nstlist = 10<br>
; ns algorithm (simple or grid) =<br>
ns_type = grid<br>
; Periodic boundary conditions: xyz or no =<br>
pbc
= xyz<br>
; nblist cut-off =<br>
rlist = 1.0<br>
domain-decomposition = no<br>
<br>
; OPTIONS FOR ELECTROSTATICS AND VDW =<br>
; Method for doing electrostatics =<br>
coulombtype
= PME ;Reaction-Field<br>
rcoulomb-switch = 0<br>
rcoulomb
= 1.0 ;2.0<br>
; Dielectric constant (DC) for cut-off or DC of reaction field =<br>
epsilon_r = 80.0<br>
epsilon_rf = 1<br>
;I have done some thing new according to mannual and warnings and error<br>
; Method for doing Van der Waals =<br>
vdwtype = Cut-off<br>
; cut-off lengths =<br>
rvdw-switch = 0<br>
rvdw
= 1.0<br>
; Apply long range dispersion corrections for Energy and Pressure =<br>
DispCorr = No<br>
; Spacing for the PME/PPPM FFT grid =<br>
fourierspacing = 0.12<br>
; FFT grid size, when a value is 0 fourierspacing will be used =<br>
fourier_nx = 0<br>
fourier_ny = 0<br>
fourier_nz = 0<br>
; EWALD/PME/PPPM parameters =<br>
pme_order = 4<br>
ewald_rtol = 1e-05<br>
ewald_geometry = 3d<br>
epsilon_surface = 0<br>
optimize_fft = yes<br>
<br>
; OPTIONS FOR WEAK COUPLING ALGORITHMS =<br>
; Temperature coupling =<br>
Tcoupl = berendsen<br>
; Groups to couple separately =<br>
tc-grps
= DPP SOL Na PIP<br>
; Time constant (ps) and reference temperature (K) =<br>
tau_t
= 0.1 0.1 0.1 0.1<br>
ref_t
= 310 310 310 310<br>
; Pressure coupling =<br>
Pcoupl = berendsen<br>
Pcoupltype = semiisotropic<br>
; Time constant (ps), compressibility (1/bar) and reference P (bar) =<br>
tau_p
= 1.0 1.0<br>
compressibility = 4.5e-5 4.5e-5<br>
ref_p
= 1.0 1.0<br>
<br>
; SIMULATED ANNEALING CONTROL =<br>
annealing = no<br>
; Time at which temperature should be zero (ps) =<br>
;zero-temp_time = 0<br>
;I have commute the above line as it has no exitance<br>
<br>
; GENERATE VELOCITIES FOR STARTUP RUN =<br>
gen_vel = yes<br>
gen_temp = 310.0<br>
gen_seed = 173529<br>
<br>
; OPTIONS FOR BONDS =<br>
constraints = all-bonds<br>
; Type of constraint algorithm =<br>
constraint_algorithm = lincs<br>
; Do not constrain the start configuration =<br>
unconstrained-start = no<br>
; Use successive overrelaxation to reduce the number of shake iterations =<br>
Shake-SOR = no<br>
; Relative tolerance of shake =<br>
shake-tol = 0.0001<br>
; Highest order in the expansion of the constraint coupling matrix =<br>
lincs_order = 4<br>
; Lincs will write a warning to the stderr if in one step a bond =<br>
; rotates over more degrees than =<br>
lincs-warnangle = 30<br>
; Convert harmonic bonds to morse potentials =<br>
morse = no<br>
<br>
; ENERGY GROUP EXCLUSIONS =<br>
; Pairs of energy groups for which all non-bonded interactions are excluded =<br>
energygrp_excl =<br>
<br>
;............................................................................................................<br>
;pulling<br>
pull = umbrella<br>
pull_geometry = direction<br>
pull_start = yes<br>
pull_ngroups = 1<br>
pull_group0 = DPP<br>
pull_group1 = PIP<br>
pull_dim = N N Y<br>
pull_k1 = 500<br>
pull_kB1 = 500<br>
pull_rate1 = 0.005<br>
pull_vec1 = 0 0 -1<br>
pull_init1 = -1.822<br>
pull_nstxout = 100<br>
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