[gmx-users] itp file
Hi, I am surprise to see that not a single .tga ( e.g., ccl4_box.tgzhttp://www.gromacs.org/@api/deki/files/32/=ccl4_box.tgz) file can be open in the http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies site? Can anyone look at this matter? Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] mdp file to calculate local pressure
Dear Sir, I am looking for local pressure where I am using gromacs-4.0.2_localpressure.tarftp://ftp.gromacs.org/pub/tmp/gromacs-4.0.2_localpressure.tar.gzpackage. I have download it from ftp://ftp.gromacs.org/pub/tmp The error which it gives during running to make tpr file, is given below --- Program grompp_mpi, VERSION 4.0.2_localpressure Source code file: gmx_fatal.c, line: 481 Fatal error: Too many warnings (1), /home/anirban/gromacs402localpressure/bin/grompp_mpi terminated. If you are sure all warnings are harmless, use the -maxwarn option. --- The warning which it gives during running to make tpr file, is given below WARNING 1 [file popc-sm-chol-assymmetric-bilayer.top, line unknown]: The largest charge group contains 11 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. Sir, now, could you please tell me where I have done mistake? In the README file, it is written that it will give localpressure.dat file automatically. But I could not do it. Thank you very much for you kind help, Anirban Polley ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] mdp file to calculate local pressure
Dear Sir, I want to calculate local pressure of the membrane (pressure variation with z -axis). I am using gromacs-localp packages. As I see that all types of errors coming from saying specifically the option of WALL in .mdp file. Actually I did not understand clearly what to do in the following options. WALLS ; Number of walls, type, atom types, densities and box-z scale factor for Ewald nwall= 2 wall_type= 9-3 wall_r_linpot= -1 wall_atomtype= wall_density = wall_ewald_zfac = 3 Could you please write clearly what to write on above options ?? I am writing here the mdp file what I am using in gromacs-localp package to calculate local pressure. integrator = sd ; stochastic dynamics - Langevin! ld_seed = -1 ; random seed for sd dt = 0.002 ; ps ! nsteps = 5 ; total 500/5=100 ps nstcomm = 1 ; freq. for cm-motion removal tinit= 0 ; starting time (ps) constraints = all-bonds ; constraint for all bond lengths constraint_algorithm = lincs ; default lincs_order = 4 ; default nstxout = 1000; T(x_out) 10 ps nstvout = 1000; T(v_out) 10 ps nstfout = 0 ; T(f_out) nstlog = 250 ; energies to log (0.5 ps) nstenergy= 250 ; energies to energy file ns_type = grid; nl type nstlist = 10 ; Freq. to update neighbour list rlist= 1.0 ; nm (cutoff for short-range nl) ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xy coulombtype = PME ;Reaction-Field ; Coulomb interactions rcoulomb = 1.0 ;2.0 ; nm (Coulomb cut-off!!) epsilon_r= 80.0; dielectric constant for reaction field vdwtype = Cut-off ; Wan der Waals interactions rvdw = 1.0 ; nm (LJ cut-off) optimize_fft = yes ; Temperature coupling Tcoupl = no ; no effect when integrator = sd tc-grps = POPC SM CHOL SOL tau_t= 0.1 0.1 0.1 0.1 ref_t= 296 296 296 296 ; Pressure coupling ;Pcoupl = no Pcoupl = berendsen Pcoupltype = semiisotropic tau_p= 1.01.0 ; ps compressibility = 4.5e-5 4.5e-5; 1/bar (water: 1 atm, 300 K) ref_p= 1.01.0 ; bar ; Generate velocites in the beginning gen_vel = yes gen_temp = 296.0 gen_seed = 173529 ;WALLS ; Number of walls, type, atom types, densities and box-z scale factor for Ewald nwall= 2 wall_type= 9-3 wall_r_linpot= -1 wall_atomtype= wall_density = wall_ewald_zfac = 3 Thanks a lot in advance. Regards, Anirban ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] mdp file to calculate local pressure
Dear Justin, I am using gromacs-localp of version 4.0.2. for the calculation of local pressure. But I could not understand what I should put in the mdp file. Because when I tried by the following below mdp file, it does not even create tpr file. I have tried by different options as for example by using Wall but failed to get local pressure profile. I thought that I have write some thing so that it can be ok for giving local pressure. Could you please correct my mdp file and write what extra term I should write in my mdp file to get local pressure. Thank you very much for your kind help. Anirban title= lipid bilayer in water cpp = /lib/cpp integrator = sd ; stochastic dynamics - Langevin! ld_seed = -1 ; random seed for sd dt = 0.002 ; ps ! nsteps = 25 ; total 500 ps nstcomm = 1 ; freq. for cm-motion removal tinit= 0 ; starting time (ps) constraints = all-bonds ; constraint for all bond lengths constraint_algorithm = lincs ; default lincs_order = 4 ; default nstxout = 5000; T(x_out) 10 ps nstvout = 5000; T(v_out) 10 ps nstfout = 0 ; T(f_out) nstlog = 250 ; energies to log (0.5 ps) nstenergy= 250 ; energies to energy file ns_type = grid; nl type nstlist = 10 ; Freq. to update neighbour list rlist= 1.0 ; nm (cutoff for short-range nl) coulombtype = Reaction-Field ; Coulomb interactions rcoulomb = 2.0 ; nm (Coulomb cut-off!!) epsilon_r= 80.0; dielectric constant for reaction field vdwtype = Cut-off ; Wan der Waals interactions rvdw = 1.0 ; nm (LJ cut-off) optimize_fft = yes ; Temperature coupling Tcoupl = no ; no effect when integrator = sd tc-grps = POPC SMCHOL SOL tau_t= 0.1 0.1 0.1 0.1 ref_t= 296 296 296 296 ; Pressure coupling ;Pcoupl = no Pcoupl = berendsen Pcoupltype = semiisotropic tau_p= 1.01.0 ; ps compressibility = 4.5e-5 4.5e-5; 1/bar (water: 1 atm, 300 K) ref_p= 1.01.0 ; bar ; Generate velocites in the beginning gen_vel = yes gen_temp = 296.0 gen_seed = 173529 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] mdp file for local pressure
Dear sir, I am calculating local pressure by gromacs-localp. My .mdp file is following integrator = sd ; stochastic dynamics - Langevin! ld_seed = -1 ; random seed for sd dt = 0.002 ; ps ! nsteps = 5 ; total 500/5=100 ps nstcomm = 1 ; freq. for cm-motion removal tinit= 0 ; starting time (ps) constraints = all-bonds ; constraint for all bond lengths constraint_algorithm = lincs ; default lincs_order = 4 ; default nstxout = 1000; T(x_out) 10 ps nstvout = 1000; T(v_out) 10 ps nstfout = 0 ; T(f_out) nstlog = 250 ; energies to log (0.5 ps) nstenergy= 250 ; energies to energy file ns_type = grid; nl type nstlist = 10 ; Freq. to update neighbour list rlist= 1.0 ; nm (cutoff for short-range nl) ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xy coulombtype = PME ;Reaction-Field ; Coulomb interactions rcoulomb = 1.0 ;2.0 ; nm (Coulomb cut-off!!) epsilon_r= 80.0; dielectric constant for reaction field vdwtype = Cut-off ; Wan der Waals interactions rvdw = 1.0 ; nm (LJ cut-off) optimize_fft = yes ; Temperature coupling Tcoupl = no ; no effect when integrator = sd tc-grps = POPC SM CHOL SOL tau_t= 0.1 0.1 0.1 0.1 ref_t= 296 296 296 296 ; Pressure coupling ;Pcoupl = no Pcoupl = berendsen Pcoupltype = semiisotropic tau_p= 1.01.0 ; ps compressibility = 4.5e-5 4.5e-5; 1/bar (water: 1 atm, 300 K) ref_p= 1.01.0 ; bar ; Generate velocites in the beginning gen_vel = yes gen_temp = 296.0 gen_seed = 173529 ;WALLS ; Number of walls, type, atom types, densities and box-z scale factor for Ewald nwall= 2 wall_type= 9-3 wall_r_linpot= -1 wall_atomtype= wall_density = wall_ewald_zfac = 3 It gives following error --- Program grompp_mpi, VERSION 4.0.2_localpressure Source code file: readir.c, line: 454 Fatal error: Expected 2 elements for wall_atomtype, found 0 --- Could you please tell me where my fault is? Thanks a lot in advance. Anirban ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] want to calculate pressure from virial
Dear Sir, I want to calculate virial, hence pressure. PV=NKT-1/3 * sum of (r * f) where r is displacement and f is internal force. Now, how can I proceed? 1. g_traj -f name.trr -af gives me force and each velocity with time? Now, question, is the force given in data is only due to internal force or total force on each atom? Am I right if I use this force and position of the atom to calculate virial. 2. If I am wrong, then please tell me how I can calculate Virial, and hence pressure. 3. I saw that g_energy -f name.edr -vis gives pressure, virial and all the stuffs. I want to know that how I can calculate it myself. 4. Can you tell me how I can calculate pressure change with z - axis where I am simulating Bilayer Membrane. Thanking You, Anirban ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] lateral stress and surface tension
Dear Sir, I am analysing bilayer membrane. Could you please tell me how I can calculate stress and surface tension of the membrane? Thanking you, Anirban ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] local pressure
Dear Sir, I would like to calculate local pressure of the bilayer membrane. Is it possible to do by new version of gromacs. could you please assist me to do it. After simulating bilayer m,embrane, I found trr, edr files. Thanking you , Anirban ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] local pressure calculation
Dear Sir, I want to calculate local pressure of the bilayer membrane. I see from the mailing list and earlier paper that it was done by gromacs-locap-3.0.2. Could you please tell me that this package will assist with gromacs 3.3.3 or gromacs 4.0.4 version. Is there any other option to calculate loacal pressure with gromacs 4.0.4 version. Thanks, Anirban ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] introducing constrain
Dear sir,
I want to put a constrain into my system. I am simulating lipid
bilayer membrane by GROMACS. I want to put a virtual wall at the z-axis in
my system so that no lipid can move through the virtual wall. In a code
language, it is just this : for lipid :if z 60
{
..
}
where two layer
of lipid is distributing from z= 20 to 70.
Again, this condition is applicable only on lipids where water molecule can
move freely according to its nature.
Could you please tell me how to do it? If any code change is necessary in
the source code of the Gromacs, then please tell me where I put the
constrain.
Thanking you,
Anirban
___
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[gmx-users] problem in pulling in gromacs 4.03
Dear sir, I want to pull a small protein molecule (GPI) which is inserted on the upper layer of the bilayer. So, I applied pull = umbrella, where umbrella potential is used between center of mass of reference group and that of pulled group. Now, as I want to pull the protein from the lipid bilayer membrane, I use the whole molecule of protein as pulled group and the whole patch of bilayer as a reference group because I thought that though I write the whole patch of bilayer as a reference group, the pull will occur w.r.t. the center of mass of the reference group. It will create no problem. Similarly, I did for the whole protein as a pulled group. I tried the pull_geometry as all distance, direction, position and it does not give any error during simulation. But, when I saw the whole trajectory in VMD, then I saw that the protein did not come out by the pulling. It is just vibrating at the same position. When I ran the simulation in NVT ensemble, the bilayer still retain its structure but when I ran it in NPT ensemble, it created crazy things, water entered inside, lipids became shrinked and so on. Can you please help me and tell me how to do it? I am eagerly waiting for your help. ; title= lipid bilayer in water cpp = /lib/cpp integrator = sd ; stochastic dynamics - Langevin! ld_seed = -1 ; random seed for sd dt = 0.002 ; ps ! nsteps = 25 ; total 500 ps nstcomm = 1 ; freq. for cm-motion removal tinit= 0 ; starting time (ps) constraints = all-bonds ; constraint for all bond lengths constraint_algorithm = lincs ; default lincs_order = 4 ; default nstxout = 5000; T(x_out) 10 ps nstvout = 5000; T(v_out) 10 ps nstfout = 0 ; T(f_out) nstlog = 250 ; energies to log (0.5 ps) nstenergy= 250 ; energies to energy file ns_type = grid; nl type nstlist = 10 ; Freq. to update neighbour list rlist= 1.0 ; nm (cutoff for short-range nl) coulombtype = PME ;Reaction-Field ; Coulomb interactions rcoulomb = 1.0 ;2.0 ; nm (Coulomb cut-off!!) epsilon_r= 80.0; dielectric constant for reaction field vdwtype = Cut-off ; Wan der Waals interactions rvdw = 1.0 ; nm (LJ cut-off) optimize_fft = yes ; Temperature coupling Tcoupl = no ; no effect when integrator = sd tc-grps = DPP SM CHOL SOL GPI tau_t= 0.1 0.1 0.1 0.1 0.1 ref_t= 310 310 310 310 310 ; Pressure coupling Pcoupl = no ;Pcoupl = berendsen Pcoupltype = semiisotropic tau_p= 1.01.0 ; ps compressibility = 4.5e-5 4.5e-5; 1/bar (water: 1 atm, 300 K) ref_p= 1.01.0 ; bar ; Generate velocites in the beginning gen_vel = yes gen_temp = 310.0 gen_seed = 173529 ; ;pulling pull = umbrella pull_geometry = direction pull_start = yes pull_ngroups = 1 pull_group0 = DPP pull_group1 = GPI pull_dim = N N Y pull_k1 = 100 ;pull_kB1 = 500 pull_rate1 = 0.0005 pull_vec1 = 0 0 1 pull_init1 = 0.0 pull_nstxout = 1 Thanking you, Anirban ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] question in pulling in gromacs 4.0
Hi , 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 = 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= 1.01.0 compressibility = 4.5e-5 4.5e-5 ref_p= 1.01.0 ; 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
[gmx-users] pulling of molecule in GROMACS 4.03
Dear Sir, I want to pull a molecule called PRO from the lipid membrane DPP. To do this I have written the .mdp file as following from the help of gromacs mannual 4.0 . But when I try to make .tpr file from the .gro file, it says that segmentation fault. Can you please write the correct .mdp file for the pulling? It will be really a great help to me. Thanking you, Anirban ; ; 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 = DPP SOL PRO ; Time constant (ps) and reference temperature (K) = tau_t= 0.1 0.1 0.1 ref_t= 310 310 310 ; Pressure coupling = Pcoupl = berendsen Pcoupltype = semiisotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p= 1.01.0 compressibility = 4.5e-5 4.5e-5 ref_p= 1.01.0 ; 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 = continuation = yes ;unconstrained-start = no ; Use successive
[gmx-users] about the run program in gromacs 4.0.3
Hi, I have run earlier in gromacs3.3.x version in parallel processor but now I have installed gromacs4.0.3. But when I want to run program in the gromacs4.0.3, it says that ... Invalid command line argument: -np ... I am surprise by seeing it because I have run the same in older version by writing /home/anirban/gromacs/grompp -np 8 -f grompp.mdp -p topol.top -c pr.gro -o pr.tpr Can you tell me what the wrong in the new version is? Why does the new version of gromacs could not connect nodes and says that -np does not valid. Regards, Anirban ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] To run in gromacs 4.0.3 in cluster
Dear Sir, In the previous older version of gromacs(3.3.x) , there is always an option -np by which I can say about the number of processors that I required parallel computation. But in the gromacs4.0.3 version, I could not find that. Can you tell me how can I run in gromacs 4.0.3 version? Previously, I used the command like following /home/anirban/gromacs/bin/grompp -np 32 -f grompp_md_nosehoover.mdp -p dppc-sm-chol-water-1-1-1.top -c dppc-sm-chol-water-1-1-1_NPT_berendsen_md.gro -o topol.tpr mpirun -np 32 /home/anirban/gromacs/bin/mdrun -v But now, what is the command to run in gromacs4.0.3 in parallel computation? Thanking you, Anirban ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] about g_wham
Hi all, Could you please tell me why g_wham does not give the correct result? After doing umbrella sampling with mdrun, I got the .pdo file which is like # UMBRELLA 3.0 # Component selection: 0 0 1 # nSkip 1 # Ref. Group 'DPP' # Nr. of pull groups 1 # Group 1 'PIP' Umb. Pos. 3.388542 Umb. Cons. 100.00 # 0.001.650988 0.0020001.650989 0.0040001.651020 0.0060001.651055 0.0080001.651139 . Now, when I try to analysis it by g_wham, I have stuck. Could you please tell me the right method? 1. g_wham -max 1.7779 -min .8988 -temp 310 -o pull_pip2_dppc.pdo. The error message is: --- Program g_wham, VERSION 3.3.3 Source code file: gmx_wham.c, line: 313 Fatal error: You need to specify a series of pdo files as input --- Question: How can I get the series of pdo file? Did it mean that I have to vary the Umb. const. and run it many times and get many .pdo files? 2. g_wham pull_pip2_dppc.pdo -max 1.7779 -min .8988 -temp 310 -o -hist The error is : Opening file pull_pip2_dppc.pdo. gzip: stdin: not in gzip format --- Program g_wham, VERSION 3.3.3 Source code file: gmx_wham.c, line: 89 Fatal error: This does not appear to be a valid pdo file --- 3. Now, I tried it by converting .gz file as an input g_wham pull_pip2_dppc.pdo.gz -max 1.7779 -min .8988 -temp 310 -o The error is: Opening file pull_pip2_dppc.pdo.gz. --- Program g_wham, VERSION 3.3.3 Source code file: gmx_wham.c, line: 89 Fatal error: This does not appear to be a valid pdo file --- Could you please tell me why it gives error again and again? What is the wrong that I have done? How Can I get the correct answer? Please, tell me the answer? I am eagerly waiting for your advise. Regards, Anirban ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Deuterium order parameter over area of membrane
Hi, I know that deuterium order parameter can be calculated by g_density but it calculate average deuterium order parameter of a type of lipid Vs. atom number of the tail of the lipid. But I want to calculate deuterium order parameter fluctuation over the area. i.e., I want to know to calculate Scd per area of the membrane. Could you tell me how to do it. Thanks, Anirban ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Thickness distribution over area of bilayer-membrane
Hi, I saw that average thickness can be measured by peak to peak distance of a electron density graph. This electron density can be calculated by g_density command. But g_density gives the average electron density of the membrane. So, I can get the average thickness of the membrane by subtracting peak to peak distance of the electron density graph. But I want to see how the thickness of the membrane is fluctuating over area. So, can you tell me how I can calculate the thickness of the membrane. Regards, Anirban ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Electron density over area
Hi, I know that electron density can be calculated by g_density. But I want to calculate electron density over area of the membrane so that I can analyze the fluctuation of the electron density with the area of the membrane. Could you tell me how to do it? Thanking you, Anirban ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] AFM by using mdrun in gromacs
Hello, I want to pull a protein from a DPPC lipid bilayer. It is written in manual that it can be done by including pull.ppa and pull.ndx with the mdrun. Now my question is how to write pull.ppa and pull.ndx.Can you tell me which parts I have to take care to make group in index file? Can you tell me how to create pull.ndx properly, because during the making of index file by giving make_ndx, I have confused which elements should be grouped ( two tails of the DPPC molecule or tails of protein molecule). regards, Anirban ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] about some question on gromacs
Hi, I have the following questions. Are there any other ways to make bilayer other than packmol? I want to make bilayer (.pdb file). I saw that in GROMACS, there is united atom model, then what are the GROMACS computes in the Deuterium order parameter? When I run the system for long time, the program suddenly crashes and says segmentation fault without giving any information for the reasons. Can you say what the probable reasons are for which the program crashes and says segmentation fault? sincerely, Anirban ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] about deuterium order parameter
Hello, I want to analyze the deuterium order parameter of a system contains DPPC, sphingomyelin(SM) and cholesterol(CHOL) and water(SOL). I read from the prevous mail that I have to make index file for sn1 and sn2. Now, my first question is what the meaning of sn1 and sn2 is. How can I assign from the .pdb file of the total system. make_ndx -f dppc20-sm20-cholesterol20-water200tolerance3-bilayer50x50x54.pdb 0 System : 3180 atoms 1 DPP : 1000 atoms 2 SM : 1000 atoms 3 CHOL: 580 atoms 4 SOL : 600 atoms nr : group ! 'name' nr name 'splitch' nrEnter: list groups 'a': atom 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr'splitat' nr'h': help 'r': residue 'res' nr 'chain' char name: group'case': case sensitive 'q': save and quit I understand that after giving the make_ndx command, I have to use above of these command ( a, t r ). But what are the full command so that I can make clear nice index file for the analysis of deuterium order parameter. In my case, for the the numbering of DPPC is like that : two tail starts from C13 to C31 and C13 to C50; SM is like that: two tails starts from C13 to C32 and C13 to C50; CHOL is like that : OH group is at 6 7and small tail comes from C21 to C29. Can you write the full command so that I can clearly understand clearly. Because, the next step I know that is g_order -f name.trr -n index.ndx -s topol.tpr -od Please, can you give the answer for me ? Sincerely, Anirban ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] about itp file making
Hi, This is first time that I am sending mail so I do not know the where I have to send for proper answer of my question. To make .itp file of a sugar molecule, what should be the gromacs force field (96/opls)? regards Anirban ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to analyze order parameter
Hi, I want to find deuterium order parameter of the system of DPPC+SM+CHOL+WATER g_order -f traj.trr -s topol.tpr -n index.ndx -dt 0.001 it gives the following error: Taking z axis as normal to the membrane Reading file topol.tpr, VERSION 3.3.3 (single precision) Using following groups: Groupname: System First atomname: C1 First atomnr 0 Groupname: DPP First atomname: C1 First atomnr 0 Groupname: SM First atomname: C1 First atomnr 1000 Groupname: CHOL First atomname: C1 First atomnr 2000 Groupname: SOL First atomname: OW First atomnr 2580 trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 Number of elements in first group: 3180 --- Program g_order, VERSION 3.3.3 Source code file: gmx_order.c, line: 360 Fatal error: grp 1 does not have same number of elements as grp 1 --- How can I analyze the order parameter my system? Can you answer my question? I don't understand what to do. Regards, Anirban ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
