[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 = 175 ; 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
RE: [gmx-users] [Fwd: Problems in pulling a molecule from the membrane]
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: schl...@uni-mainz.de To: gmx-users@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 = 175 ; 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 Pre
