Re: [gmx-users] Grompp note
Could you tell how can I get rid of following warning? WARNING 1 [file test.top, line 263]: The bond in molecule-type BMI between atoms 10 C10 and 23 H23 has an estimated oscillational period of 1.2e-03 ps, which is less than 5 times the time step of 1.0e-03 ps. Maybe you forgot to change the constraints mdp option. > > On 10/31/13 10:30 AM, Nilesh Dhumal wrote: >> Hello, >> >> I am running a equilibration simulation for ionic liquids at 400 K. >> >> I am getting following note. >> >> The sum of the two largest charge group radii (0.213127) is larger >> than >>rlist (1.00) - rvdw (0.90) >> >> Could you tell what is the problem? I am using Gromacs VERSION 4.5.5 . >> > > http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb > > Also see the numerous discussions on this topic in the list archive. > > -Justin > >> >> I used the following mdp file. >> >> ; RUN CONTROL PARAMETERS = >> integrator = sd >> ; start time and timestep in ps = >> tinit= 0 >> dt = 0.001 >> nsteps = 20 >> ; number of steps for center of mass motion removal = >> nstcomm = 100 >> ; OUTPUT CONTROL OPTIONS = >> ; Output frequency for coords (x), velocities (v) and forces (f) = >> nstxout = 0 >> nstvout = 0 >> nstfout = 0 >> ; Output frequency for energies to log file and energy file = >> nstlog = 5000 >> nstenergy= 1000 >> ; Output frequency and precision for xtc file = >> nstxtcout= 5000 >> xtc-precision= 1000 >> ; NEIGHBORSEARCHING PARAMETERS = >> ; nblist update frequency = >> nstlist = 10 >> ; ns algorithm (simple or grid) = >> ns_type = grid >> ;OPTIONS FOR TEMPERATURE COUPLING >> tc_grps = system >> tau_t= 0.1 >> ref_t= 400 >> ;OPTIONS FOR PRESSURE COUPLING >> Pcoupl = berendsen >> tau_p= 0.5 >> compressibility = 4.5e-05 >> ref_p= 1.0 >> ; OPTIONS FOR BONDS = >> constraints = hbonds >> ; Type of constraint algorithm = >> constraint-algorithm = Lincs >> ; Do not constrain the start configuration = >> unconstrained-start = no >> ; Relative tolerance of shake = >> shake-tol= 0.0001 >> ; Highest order in the expansion of the constraint coupling matrix = >> lincs-order = 12 >> ; Lincs will write a warning to the stderr if in one step a bond = >> ; rotates over more degrees than = >> lincs-warnangle = 30 >> >> ; Periodic boundary conditions: xyz or none = >> pbc = xyz >> ; nblist cut-off = >> rlist= 1.0 >> domain-decomposition = no >> ; OPTIONS FOR ELECTROSTATICS AND VDW = >> ; Method for doing electrostatics = >> coulombtype = pme >> ;rcoulomb-switch = 0 >> rcoulomb = 1.0 >> ; Dielectric constant (DC) for cut-off or DC of reaction field = >> epsilon-r= 1 >> ; Method for doing Van der Waals = >> vdw-type = switch >> ; cut-off lengths= >> rvdw-switch = 0.8 >> rvdw = 0.9 >> ; Apply long range dispersion corrections for Energy and Pressure = >> DispCorr = EnerPres >> ; Spacing for the PME/PPPM FFT grid = >> fourierspacing = 0.1 >> ; 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= 6 >> ewald_rtol = 1e-06 >> epsilon_surface = 0 >> optimize_fft = no >> ; Free energy control stuff >> free_energy = no >> >> >> Nilesh >> >> >> >> > > -- > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.e
[gmx-users] Grompp note
Hello, I am running a equilibration simulation for ionic liquids at 400 K. I am getting following note. The sum of the two largest charge group radii (0.213127) is larger than rlist (1.00) - rvdw (0.90) Could you tell what is the problem? I am using Gromacs VERSION 4.5.5 . I used the following mdp file. ; RUN CONTROL PARAMETERS = integrator = sd ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps = 20 ; number of steps for center of mass motion removal = nstcomm = 100 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 0 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 5000 nstenergy= 1000 ; Output frequency and precision for xtc file = nstxtcout= 5000 xtc-precision= 1000 ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ;OPTIONS FOR TEMPERATURE COUPLING tc_grps = system tau_t= 0.1 ref_t= 400 ;OPTIONS FOR PRESSURE COUPLING Pcoupl = berendsen tau_p= 0.5 compressibility = 4.5e-05 ref_p= 1.0 ; OPTIONS FOR BONDS = constraints = hbonds ; Type of constraint algorithm = constraint-algorithm = Lincs ; Do not constrain the start configuration = unconstrained-start = no ; Relative tolerance of shake = shake-tol= 0.0001 ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 12 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs-warnangle = 30 ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist= 1.0 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = pme ;rcoulomb-switch = 0 rcoulomb = 1.0 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r= 1 ; Method for doing Van der Waals = vdw-type = switch ; cut-off lengths= rvdw-switch = 0.8 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.1 ; 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= 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no ; Free energy control stuff free_energy = no Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Box size increases in NPT
Hello, I am running a NPT simulation for cyclopropylchloride(1) in 50%water(100)+50%ethanol(100) using opls force field parameter . After equilibration box size increases from 20 A to 70 A. I used the following mdp file. ; RUN CONTROL PARAMETERS = integrator = sd ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps = 5 ; number of steps for center of mass motion removal = nstcomm = 100 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 0 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 500 nstenergy= 100 ; Output frequency and precision for xtc file = nstxtcout= 5000 xtc-precision= 1000 ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ;OPTIONS FOR TEMPERATURE COUPLING tc_grps = system tau_t= 0.1 ref_t= 290;350 ;OPTIONS FOR PRESSURE COUPLING Pcoupl = berendsen tau_p= 0.5 compressibility = 4.5e-05 ref_p= 1.0 ; OPTIONS FOR BONDS = constraints = hbonds ; Type of constraint algorithm = constraint-algorithm = Lincs ; Do not constrain the start configuration = unconstrained-start = no ; Relative tolerance of shake = shake-tol= 0.0001 ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 12 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs-warnangle = 30 ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist= 0.9 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = pme ;rcoulomb-switch = 0 rcoulomb = 0.9 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r= 1 ; Method for doing Van der Waals = vdw-type = switch ; cut-off lengths= rvdw-switch = 0.8 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.1 ; 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= 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no ; Free energy control stuff free_energy = no Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 0.826223 nm
Thanks for you reply. I am doing simulation for ionic liquids BMIM + CL. Total number of atoms are 3328. Nilesh > Assuming you're using LINCS, from the manual: > "With domain decomposition, the cell size is limited by the distance > spanned by *lincs-order*+1 constraints." > Assuming a default lincs-order (4), 0.82nm seems a fairly sane distance > for > 5 bonds. > > Which means that you're probably using too many nodes for the size of your > system. > > Hope that helps. If it doesn't you'll need to provide some information > about your system. > > -Trayder > > > > On Thu, Oct 17, 2013 at 1:27 PM, Nilesh Dhumal > wrote: > >> Hello, >> >> I am getting the following error for simulation. I am using Gromacs >> VERSION 4.5.5 and running on 24 processors. >> >> Should I reduce the number of processor or the problem is in bonded >> parameters. If I use -nt 1 option. I could run the simulation. >> >> Fatal error: >> There is no domain decomposition for 16 nodes that is compatible with >> the >> given box and a minimum cell size of 0.826223 nm >> Change the number of nodes or mdrun option -rdd or -dds >> Look in the log file for details on the domain decomposition >> >> >> Nilesh >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >> > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 0.826223 nm
Hello, I am getting the following error for simulation. I am using Gromacs VERSION 4.5.5 and running on 24 processors. Should I reduce the number of processor or the problem is in bonded parameters. If I use -nt 1 option. I could run the simulation. Fatal error: There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 0.826223 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match
Thanks. I have total 128 EMI and 128 ETS. To find the solution I test for 2 EMI and 2 ETS. How can I define for 128 EMI and 128 ETS ? Nilesh > > On 9/22/13 9:18 PM, Nilesh Dhumal wrote: >> Sorry to paste big files here. (.pdb file and processed.top ) >> >> >> pdb file. >> >> TITLE Protein >> REMARKTHIS IS A SIMULATION BOX >> CRYST1 34.775 34.775 34.775 90.00 90.00 90.00 P 1 1 >> MODEL1 >> ATOM 1 C EMI 1 4.659 30.489 15.747 1.00 0.00 >> ATOM 2 C2 EMI 1 5.238 30.284 14.495 1.00 0.00 >> ATOM 3 N3 EMI 1 6.415 30.946 14.495 1.00 0.00 >> ATOM 4 C4 EMI 1 6.627 31.499 15.682 1.00 0.00 >> ATOM 5 N5 EMI 1 5.595 31.153 16.470 1.00 0.00 >> ATOM 6 C6 EMI 1 5.462 31.463 17.884 1.00 0.00 >> ATOM 7 C7 EMI 1 4.501 30.509 18.615 1.00 0.00 >> ATOM 8 C8 EMI 1 7.321 30.993 13.363 1.00 0.00 >> ATOM 9 H9 EMI 1 3.672 30.193 16.130 1.00 0.00 >> ATOM 10 H10 EMI 1 4.839 29.853 13.640 1.00 0.00 >> ATOM 11 H11 EMI 1 7.514 32.004 16.038 1.00 0.00 >> ATOM 12 H12 EMI 1 7.951 31.796 13.329 1.00 0.00 >> ATOM 13 H13 EMI 1 7.967 30.145 13.270 1.00 0.00 >> ATOM 14 H14 EMI 1 6.890 31.170 12.362 1.00 0.00 >> ATOM 15 H15 EMI 1 5.214 32.491 18.125 1.00 0.00 >> ATOM 16 H16 EMI 1 6.495 31.335 18.302 1.00 0.00 >> ATOM 17 H17 EMI 1 4.834 29.492 18.590 1.00 0.00 >> ATOM 18 H18 EMI 1 4.337 30.767 19.685 1.00 0.00 >> ATOM 19 H19 EMI 1 3.486 30.669 18.338 1.00 0.00 >> ATOM 20 S20 ETS 2 13.817 2.976 33.669 1.00 0.00 >> ATOM 21 O21 ETS 2 15.031 2.685 34.347 1.00 0.00 >> ATOM 22 O22 ETS 2 14.005 3.313 32.237 1.00 0.00 >> ATOM 23 O23 ETS 2 12.775 1.970 33.860 1.00 0.00 >> ATOM 24 O24 ETS 2 13.303 4.314 34.278 1.00 0.00 >> ATOM 25 C25 ETS 2 12.361 5.280 33.781 1.00 0.00 >> ATOM 26 C26 ETS 2 12.277 6.501 34.666 1.00 0.00 >> ATOM 27 H27 ETS 2 12.582 5.675 32.806 1.00 0.00 >> ATOM 28 H28 ETS 2 11.377 4.787 33.550 1.00 0.00 >> ATOM 29 H29 ETS 2 11.686 6.245 35.492 1.00 0.00 >> ATOM 30 H30 ETS 2 13.256 6.810 34.975 1.00 0.00 >> ATOM 31 H31 ETS 2 11.856 7.349 34.171 1.00 0.00 >> ATOM 32 C EMI 3 25.075 29.706 5.816 1.00 0.00 >> ATOM 33 C2 EMI 3 24.256 29.876 6.894 1.00 0.00 >> ATOM 34 N3 EMI 3 25.074 30.288 7.940 1.00 0.00 >> ATOM 35 C4 EMI 3 26.335 30.336 7.464 1.00 0.00 >> ATOM 36 N5 EMI 3 26.369 29.867 6.216 1.00 0.00 >> ATOM 37 C6 EMI 3 27.586 29.761 5.460 1.00 0.00 >> ATOM 38 C7 EMI 3 27.397 29.088 4.106 1.00 0.00 >> ATOM 39 C8 EMI 3 24.601 30.404 9.351 1.00 0.00 >> ATOM 40 H9 EMI 3 24.815 29.446 4.790 1.00 0.00 >> ATOM 41 H10 EMI 3 23.203 29.817 6.920 1.00 0.00 >> ATOM 42 H11 EMI 3 27.238 30.558 8.074 1.00 0.00 >> ATOM 43 H12 EMI 3 24.321 29.435 9.759 1.00 0.00 >> ATOM 44 H13 EMI 3 25.411 30.876 9.880 1.00 0.00 >> ATOM 45 H14 EMI 3 23.735 31.092 9.515 1.00 0.00 >> ATOM 46 H15 EMI 3 28.216 29.130 6.169 1.00 0.00 >> ATOM 47 H16 EMI 3 28.027 30.763 5.434 1.00 0.00 >> ATOM 48 H17 EMI 3 26.886 29.695 3.344 1.00 0.00 >> ATOM 49 H18 EMI 3 28.366 28.886 3.715 1.00 0.00 >> ATOM 50 H19 EMI 3 26.842 28.200 3.880 1.00 0.00 >> ATOM 51 S20 ETS 4 26.876 17.203 7.791 1.00 0.00 >> ATOM 52 O21 ETS 4 28.030 16.750 7.061 1.00 0.00 >> ATOM 53 O22 ETS 4 25.656 16.428 7.528 1.00 0.00 >> ATOM 54 O23 ETS 4 27.112 17.470 9.202 1.00 0.00 >> ATOM 55 O24 ETS 4 26.578 18.733 7.129 1.00 0.00 >> ATOM 56 C25 ETS 4 26.215 18.995 5.843 1.00 0.00 >> ATOM 57 C26 ETS 4 27.436 19.133 4.921 1.00 0.00 >> ATOM 58 H27 ETS 4 25.607 18.170 5.486 1.00 0.00 >> ATOM 59 H28 ETS 4 25.530 19.872 5.774 1.00 0.00 >> ATOM 60 H29
Re: [gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match
47373850 3 52515556 3 53515556 3 54515556 3 51555657 3 51555658 3 51555659 3 55565760 3 55565761 3 55565762 3 58565760 3 58565761 3 58565762 3 59565760 3 59565761 3 59565762 3 ; Include Position restraint file ; Include water topology ;#include "spc.itp" ; Include generic topology for ions ;#include "ions.itp" [ system ] ; Name Protein [ molecules ] ; Compound#mols EMI 2 ETS 2 Nilesh > On 9/22/13 7:13 PM, Nilesh Dhumal wrote: >> Hello, >> >> I am doing energy minimization for my system. I am getting following >> warnings >> >> Warning: atom name 20 in p2.top and p2.pdb does not match (C - S20) >> Warning: atom name 21 in p2.top and p2.pdb does not match (C2 - O21) >> Warning: atom name 22 in p2.top and p2.pdb does not match (N3 - O22) >> Warning: atom name 23 in p2.top and p2.pdb does not match (C4 - O23) >> Warning: atom name 24 in p2.top and p2.pdb does not match (N5 - O24) >> Warning: atom name 25 in p2.top and p2.pdb does not match (C6 - C25) >> Warning: atom name 26 in p2.top and p2.pdb does not match (C7 - C26) >> Warning: atom name 27 in p2.top and p2.pdb does not match (C8 - H27) >> Warning: atom name 28 in p2.top and p2.pdb does not match (H9 - H28) >> Warning: atom name 29 in p2.top and p2.pdb does not match (H10 - H29) >> Warning: atom name 30 in p2.top and p2.pdb does not match (H11 - H30) >> Warning: atom name 31 in p2.top and p2.pdb does not match (H12 - H31) >> Warning: atom name 32 in p2.top and p2.pdb does not match (H13 - C) >> Warning: atom name 33 in p2.top and p2.pdb does not match (H14 - C2) >> Warning: atom name 34 in p2.top and p2.pdb does not match (H15 - N3) >> Warning: atom name 35 in p2.top and p2.pdb does not match (H16 - C4) >> Warning: atom name 36 in p2.top and p2.pdb does not match (H17 - N5) >> Warning: atom name 37 in p2.top and p2.pdb does not match (H18 - C6) >> Warning: atom name 38 in p2.top and p2.pdb does not match (H19 - C7) >> Warning: atom name 39 in p2.top and p2.pdb does not match (S20 - C8) >> >> >> Here is .pdb file >> >> TITLE Protein >> REMARKTHIS IS A SIMULATION BOX >> CRYST1 34.775 34.775 34.775 90.00 90.00 90.00 P 1 1 >> MODEL1 >> ATOM 1 C EMI 1 4.659 30.489 15.747 1.00 0.00 >> ATOM 2 C2 EMI 1 5.238 30.284 14.495 1.00 0.00 >> ATOM 3 N3 EMI 1 6.415 30.946 14.495 1.00 0.00 >> ATOM 4 C4 EMI 1 6.627 31.499 15.682 1.00 0.00 >> ATOM 5 N5 EMI 1 5.595 31.153 16.470 1.00 0.00 >> ATOM 6 C6 EMI 1 5.462 31.463 17.884 1.00 0.00 >> ATOM 7 C7 EMI 1 4.501 30.509 18.615 1.00 0.00 >> ATOM 8 C8 EMI 1 7.321 30.993 13.363 1.00 0.00 >> ATOM 9 H9 EMI 1 3.672 30.193 16.130 1.00 0.00 >> ATOM 10 H10 EMI 1 4.839 29.853 13.640 1.00 0.00 >> ATOM 11 H11 EMI 1 7.514 32.004 16.038 1.00 0.00 >> ATOM 12 H12 EMI 1 7.951 31.796 13.329 1.00 0.00 >> ATOM 13 H13 EMI 1 7.967 30.145 13.270 1.00 0.00 >> ATOM 14 H14 EMI 1 6.890 31.170 12.362 1.00 0.00 >> ATOM 15 H15 EMI 1 5.214 32.491 18.125 1.00 0.00 >> ATOM 16 H16 EMI 1 6.495 31.335 18.302 1.00 0.00 >> ATOM 17 H17 EMI 1 4.834 29.492 18.590 1.00 0.00 >> ATOM 18 H18 EMI 1 4.337 30.767 19.685 1.00 0.00 >> ATOM 19 H19 EMI 1 3.486 30.669 18.338 1.00 0.00 >> ATOM 20 S20 ETS 2 13.817 2.976 33.669 1.00 0.00 >> ATOM 21 O21 ETS 2 15.031 2.685 34.347 1.00 0.00 >> ATOM 22 O22 ETS 2 14.005 3.313 32.237 1.00 0.00 >> ATOM 23 O23 ETS 2 12.775 1.970 33.860 1.00 0.00 >> ATOM 24 O24 ETS 2 13.303 4.314 34.278 1.00 0.00 >> ATOM 25 C25 ETS 2 12.361 5.280 33.781 1.00 0.00 >> ATOM 26 C26 ETS 2 12.277 6.501 34.666 1.00 0.00 >> ATOM 27 H27 ETS 2 12.582 5.675 32.806 1.00 0.00 >> ATOM 28 H28 ETS 2 11.377 4.787 33.550 1.00 0.00 >> ATOM 29 H29 ETS 2 11.686 6.245 35.492 1.00 0.00 >> ATOM 30 H30 ETS 2 13.256 6.810 34.975
[gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match
Hello, I am doing energy minimization for my system. I am getting following warnings Warning: atom name 20 in p2.top and p2.pdb does not match (C - S20) Warning: atom name 21 in p2.top and p2.pdb does not match (C2 - O21) Warning: atom name 22 in p2.top and p2.pdb does not match (N3 - O22) Warning: atom name 23 in p2.top and p2.pdb does not match (C4 - O23) Warning: atom name 24 in p2.top and p2.pdb does not match (N5 - O24) Warning: atom name 25 in p2.top and p2.pdb does not match (C6 - C25) Warning: atom name 26 in p2.top and p2.pdb does not match (C7 - C26) Warning: atom name 27 in p2.top and p2.pdb does not match (C8 - H27) Warning: atom name 28 in p2.top and p2.pdb does not match (H9 - H28) Warning: atom name 29 in p2.top and p2.pdb does not match (H10 - H29) Warning: atom name 30 in p2.top and p2.pdb does not match (H11 - H30) Warning: atom name 31 in p2.top and p2.pdb does not match (H12 - H31) Warning: atom name 32 in p2.top and p2.pdb does not match (H13 - C) Warning: atom name 33 in p2.top and p2.pdb does not match (H14 - C2) Warning: atom name 34 in p2.top and p2.pdb does not match (H15 - N3) Warning: atom name 35 in p2.top and p2.pdb does not match (H16 - C4) Warning: atom name 36 in p2.top and p2.pdb does not match (H17 - N5) Warning: atom name 37 in p2.top and p2.pdb does not match (H18 - C6) Warning: atom name 38 in p2.top and p2.pdb does not match (H19 - C7) Warning: atom name 39 in p2.top and p2.pdb does not match (S20 - C8) Here is .pdb file TITLE Protein REMARKTHIS IS A SIMULATION BOX CRYST1 34.775 34.775 34.775 90.00 90.00 90.00 P 1 1 MODEL1 ATOM 1 C EMI 1 4.659 30.489 15.747 1.00 0.00 ATOM 2 C2 EMI 1 5.238 30.284 14.495 1.00 0.00 ATOM 3 N3 EMI 1 6.415 30.946 14.495 1.00 0.00 ATOM 4 C4 EMI 1 6.627 31.499 15.682 1.00 0.00 ATOM 5 N5 EMI 1 5.595 31.153 16.470 1.00 0.00 ATOM 6 C6 EMI 1 5.462 31.463 17.884 1.00 0.00 ATOM 7 C7 EMI 1 4.501 30.509 18.615 1.00 0.00 ATOM 8 C8 EMI 1 7.321 30.993 13.363 1.00 0.00 ATOM 9 H9 EMI 1 3.672 30.193 16.130 1.00 0.00 ATOM 10 H10 EMI 1 4.839 29.853 13.640 1.00 0.00 ATOM 11 H11 EMI 1 7.514 32.004 16.038 1.00 0.00 ATOM 12 H12 EMI 1 7.951 31.796 13.329 1.00 0.00 ATOM 13 H13 EMI 1 7.967 30.145 13.270 1.00 0.00 ATOM 14 H14 EMI 1 6.890 31.170 12.362 1.00 0.00 ATOM 15 H15 EMI 1 5.214 32.491 18.125 1.00 0.00 ATOM 16 H16 EMI 1 6.495 31.335 18.302 1.00 0.00 ATOM 17 H17 EMI 1 4.834 29.492 18.590 1.00 0.00 ATOM 18 H18 EMI 1 4.337 30.767 19.685 1.00 0.00 ATOM 19 H19 EMI 1 3.486 30.669 18.338 1.00 0.00 ATOM 20 S20 ETS 2 13.817 2.976 33.669 1.00 0.00 ATOM 21 O21 ETS 2 15.031 2.685 34.347 1.00 0.00 ATOM 22 O22 ETS 2 14.005 3.313 32.237 1.00 0.00 ATOM 23 O23 ETS 2 12.775 1.970 33.860 1.00 0.00 ATOM 24 O24 ETS 2 13.303 4.314 34.278 1.00 0.00 ATOM 25 C25 ETS 2 12.361 5.280 33.781 1.00 0.00 ATOM 26 C26 ETS 2 12.277 6.501 34.666 1.00 0.00 ATOM 27 H27 ETS 2 12.582 5.675 32.806 1.00 0.00 ATOM 28 H28 ETS 2 11.377 4.787 33.550 1.00 0.00 ATOM 29 H29 ETS 2 11.686 6.245 35.492 1.00 0.00 ATOM 30 H30 ETS 2 13.256 6.810 34.975 1.00 0.00 ATOM 31 H31 ETS 2 11.856 7.349 34.171 1.00 0.00 ATOM 32 C EMI 3 25.075 29.706 5.816 1.00 0.00 ATOM 33 C2 EMI 3 24.256 29.876 6.894 1.00 0.00 and .top file is [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_561 1EMI C 1 -0.13 12.011 ; qtot -0.13 2 opls_561 1EMI C2 2 -0.13 12.011 ; qtot -0.26 3 opls_557 1EMI N3 3 0.1514.0067 ; qtot -0.11 4 opls_558 1EMI C4 4 -0.11 12.011 ; qtot -0.22 5 opls_557 1EMI N5 5 0.1514.0067 ; qtot -0.07 6 opls_136 1EMI C6 6 -0.05 12.011 ; qtot -0.12 7 opls_135 1EMI C7 7 -0.17 12.011 ; qtot -0.29 8 opls_135 1EMI C8 8 -0.17 12.011 ; qtot -0.46 9 opls_564 1EMI H9 9 0.21 1.008 ; qtot -0.25 10 opls_564 1EMIH10 9 0.21 1.008 ; qtot -0.04 11 opls_563 1EMIH11 9 0.21 1.008 ; qtot 0.17 12 opls_140 1EMIH12 10 0.13 1.008 ; qtot 0.3 13 opls_140 1EMIH13
RE: [gmx-users] g_current
Did you get chance to take look at the g_current? why it is -inf (infinity) at the end with -mc option (mc.xvg). > > >> -Original Message- >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> boun...@gromacs.org] On Behalf Of Nilesh Dhumal >> Sent: Tuesday, July 09, 2013 5:06 AM >> To: Discussion list for GROMACS users >> Subject: RE: [gmx-users] g_current >> >> Thanks for reply. >> >> Still I have a question why it is -inf (infinity) at the end. > > This is a good question. At the moment, the only thing I can imagine is a > faulty normalization, because the value of the integral at t=0 equals > always > zero. However, if you integrate the first row with another tool, such as > g_analyze for example, the same values as in the second row show appear. > > As soon as I have some time left, I will take a look at the code and > report > back. > > /Flo > >> >> Nilesh >> >> > Hi, >> > >> > I would say the problem is too less statistics. In the paper where >> the >> > tool >> > was introduced, a simulation of 100ns has been performed in order to >> > achieved sufficient sampling. >> > >> > The order of magnitude is given due to the units. >> > >> > Simulate for a longer time to get rid of the noise. Calculating these > kind >> > of correlations functions is really not a simple task. >> > >> > Schroeder et al. have published an article about fitting of dielectric >> > spectra for ionic liquids, where this problem is discussed in detail. >> > >> > Cheers, >> > Flo >> > >> >> -Original Message- >> >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> >> boun...@gromacs.org] On Behalf Of Nilesh Dhumal >> >> Sent: Monday, July 08, 2013 10:32 PM >> >> To: gmx-users@gromacs.org >> >> Subject: [gmx-users] g_current >> >> >> >> Hello, >> >> I am calculating the correlation of rotational and translation dipole >> >> moment of ionic liquids. I run the 1 ns simulation and saved the >> >> trajectory at 1 fs. >> >> >> >> g_current -f md.trr -s md.tpr -n index.ndx -mc >> >> >> >> I selected "system" group. >> >> >> >> Here I pasted the initial j(t) vales and the final value is infinity. >> >> >> >> # This file was created Sun Jul 7 20:51:59 2013 >> >> # by the following command: >> >> # g_current -f md.trr -s md.tpr -e 10.0 -mc >> >> # >> >> # g_current is part of G R O M A C S: >> >> # >> >> # Gallium Rubidium Oxygen Manganese Argon Carbon Silicon >> >> # >> >> @title "M\sD\N - current autocorrelation function" >> >> @xaxis label "Time (ps)" >> >> @yaxis label "< M\sD\N (0)\c7\CJ(t) > (e nm/ps)\S2" >> >> @TYPE xy >> >> # time M_D(0) J(t) acf Integral acf >> >> 0.000 -5.20584e-15 0 >> >> 0.001 -6.97466e-15-1.42702e-17 >> >> 0.002 -6.97511e-15-5.25081e-17 >> >> 0.003 -6.97474e-15-9.07484e-17 >> >> 0.004 -6.97391e-15-1.28987e-16 >> >> >> >> >> >> >> >> Why final value is infinity? If I do autocorrelation function of >> these >> >> values, I get all values 0. >> >> >> >> Why J(t)values are in range of e-15? >> >> >> >> Nilesh >> >> >> >> >> >> >> >> -- >> >> gmx-users mailing listgmx-users@gromacs.org >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> >> * Please search the archive at >> >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >> > >> > -- >> > gmx-users mailing listgmx-users@gromacs.org >> > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > * Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/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.
[gmx-users] fluctuation of energy in rerun
Hello I am running a simulation with charge and without charge for 128 pairs of bmim-tf2n ioinc liquids. This is the command for the original run without charge mdrun -s gs.tpr -o gs.trr -c 0.pdb -e gs.edr -g gs.log -pd -nt 8 This is the command for the rerun with charge mdrun -s es.tpr -o es.trr -c 0.pdb -e es.edr -g es.log -rerun gs.trr -pd -nt 8 In the original trajectory, the energy of the system fluctuates around 5000 kJ/mol. In the rerun trajectory, the energy of the system also mostly fluctuates around 5000 kJ/mol, but sometimes it jumps to 10^13 or 10^-13. In the most recent run (20 ns), 16 data points out of 200 were extremely large. Checking the trajectory files, it seems like caused by molecule stretching across the pbc. Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] qm-mm calculation
Hello, I am trying to run the qm-mm gas phase calculations for my system. I am using following in md.mdp file. title = cpeptide MD cpp = /usr/bin/cpp integrator = md dt = 0.001; ps ! nsteps = 500 ; total 5 ps. nstcomm = 1 nstxout = 1 nstvout = 1 nstfout = 1 nstlist = 1 ns_type = simple rlist = 0.0 rcoulomb= 0.0 rvdw= 0.0 coulombtype = cut-off vdwtype = cut-off pbc = no fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on Tcoupl = nose-hoover tau_t = 0.1 tc-grps =system ref_t = 350 ; Pressure coupling is on Pcoupl = no ;Parrinello-Rahman pcoupltype = isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 350.0 gen_seed= 173529 QMMM = yes QMMM-grps= System QMmethod = RHF QMbasis = 3-21G QMcharge = 0 QMmult = 1 I could run the grompp and for mdrun I am getting following error. Back Off! I just backed up md.log to ./#md.log.2# Reading file 1.tpr, VERSION 4.0.7 (single precision) QM/MM calculation requested. there we go! Layer 0 nr of QM atoms 32 QMlevel: RHF/3-21G number of CPUs for gaussian = 1 memory for gaussian = 5000 accuracy in l510 = 8 NOT using cp-mcscf in l1003 Level of SA at start = 0 [c63:25888] *** Process received signal *** [c63:25888] Signal: Segmentation fault (11) [c63:25888] Signal code: Address not mapped (1) [c63:25888] Failing at address: (nil) [c63:25888] [ 0] /lib64/libpthread.so.0 [0x2b2d89ac1a90] [c63:25888] [ 1] /lib64/libc.so.6(strlen+0x40) [0x2b2d89d4b590] [c63:25888] [ 2] /lib64/libc.so.6(fputs+0x1e) [0x2b2d89d33dde] [c63:25888] [ 3] mdrun(init_gaussian+0x4c3) [0x51e993] [c63:25888] [ 4] mdrun(init_QMMMrec+0xef8) [0x517578] [c63:25888] [ 5] mdrun(mdrunner+0x1019) [0x42e109] [c63:25888] [ 6] mdrun(main+0x3c5) [0x434b95] [c63:25888] [ 7] /lib64/libc.so.6(__libc_start_main+0xe6) [0x2b2d89ced586] [c63:25888] [ 8] mdrun [0x415cb9] [c63:25888] *** End of error message *** Segmentation fault Could you tell what is the problem. Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] qm-mm calculation
Hello, I am trying to run the qm-mm gas phase calculations for my system. I am using following in md.mdp file. title = cpeptide MD cpp = /usr/bin/cpp integrator = md dt = 0.001; ps ! nsteps = 500 ; total 5 ps. nstcomm = 1 nstxout = 1 nstvout = 1 nstfout = 1 nstlist = 1 ns_type = simple rlist = 0.0 rcoulomb= 0.0 rvdw= 0.0 coulombtype = cut-off vdwtype = cut-off pbc = no fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on Tcoupl = nose-hoover tau_t = 0.1 tc-grps =system ref_t = 350 ; Pressure coupling is on Pcoupl = no ;Parrinello-Rahman pcoupltype = isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 350.0 gen_seed= 173529 QMMM = yes QMMM-grps= System QMmethod = RHF QMbasis = 3-21G QMcharge = 0 QMmult = 1 I could run the grompp and for mdrun I am getting following error. Back Off! I just backed up md.log to ./#md.log.2# Reading file 1.tpr, VERSION 4.0.7 (single precision) QM/MM calculation requested. there we go! Layer 0 nr of QM atoms 32 QMlevel: RHF/3-21G number of CPUs for gaussian = 1 memory for gaussian = 5000 accuracy in l510 = 8 NOT using cp-mcscf in l1003 Level of SA at start = 0 [c63:25888] *** Process received signal *** [c63:25888] Signal: Segmentation fault (11) [c63:25888] Signal code: Address not mapped (1) [c63:25888] Failing at address: (nil) [c63:25888] [ 0] /lib64/libpthread.so.0 [0x2b2d89ac1a90] [c63:25888] [ 1] /lib64/libc.so.6(strlen+0x40) [0x2b2d89d4b590] [c63:25888] [ 2] /lib64/libc.so.6(fputs+0x1e) [0x2b2d89d33dde] [c63:25888] [ 3] mdrun(init_gaussian+0x4c3) [0x51e993] [c63:25888] [ 4] mdrun(init_QMMMrec+0xef8) [0x517578] [c63:25888] [ 5] mdrun(mdrunner+0x1019) [0x42e109] [c63:25888] [ 6] mdrun(main+0x3c5) [0x434b95] [c63:25888] [ 7] /lib64/libc.so.6(__libc_start_main+0xe6) [0x2b2d89ced586] [c63:25888] [ 8] mdrun [0x415cb9] [c63:25888] *** End of error message *** Segmentation fault Could you tell what is the problem. Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] g_current
Thanks for reply. Still I have a question why it is -inf (infinity) at the end. Nilesh > Hi, > > I would say the problem is too less statistics. In the paper where the > tool > was introduced, a simulation of 100ns has been performed in order to > achieved sufficient sampling. > > The order of magnitude is given due to the units. > > Simulate for a longer time to get rid of the noise. Calculating these kind > of correlations functions is really not a simple task. > > Schroeder et al. have published an article about fitting of dielectric > spectra for ionic liquids, where this problem is discussed in detail. > > Cheers, > Flo > >> -Original Message- >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> boun...@gromacs.org] On Behalf Of Nilesh Dhumal >> Sent: Monday, July 08, 2013 10:32 PM >> To: gmx-users@gromacs.org >> Subject: [gmx-users] g_current >> >> Hello, >> I am calculating the correlation of rotational and translation dipole >> moment of ionic liquids. I run the 1 ns simulation and saved the >> trajectory at 1 fs. >> >> g_current -f md.trr -s md.tpr -n index.ndx -mc >> >> I selected "system" group. >> >> Here I pasted the initial j(t) vales and the final value is infinity. >> >> # This file was created Sun Jul 7 20:51:59 2013 >> # by the following command: >> # g_current -f md.trr -s md.tpr -e 10.0 -mc >> # >> # g_current is part of G R O M A C S: >> # >> # Gallium Rubidium Oxygen Manganese Argon Carbon Silicon >> # >> @title "M\sD\N - current autocorrelation function" >> @xaxis label "Time (ps)" >> @yaxis label "< M\sD\N (0)\c7\CJ(t) > (e nm/ps)\S2" >> @TYPE xy >> # time M_D(0) J(t) acf Integral acf >> 0.000 -5.20584e-15 0 >> 0.001 -6.97466e-15-1.42702e-17 >> 0.002 -6.97511e-15-5.25081e-17 >> 0.003 -6.97474e-15-9.07484e-17 >> 0.004 -6.97391e-15-1.28987e-16 >> >> >> >> Why final value is infinity? If I do autocorrelation function of these >> values, I get all values 0. >> >> Why J(t)values are in range of e-15? >> >> Nilesh >> >> >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_current
Hello, I am calculating the correlation of rotational and translation dipole moment of ionic liquids. I run the 1 ns simulation and saved the trajectory at 1 fs. g_current -f md.trr -s md.tpr -n index.ndx -mc I selected "system" group. Here I pasted the initial j(t) vales and the final value is infinity. # This file was created Sun Jul 7 20:51:59 2013 # by the following command: # g_current -f md.trr -s md.tpr -e 10.0 -mc # # g_current is part of G R O M A C S: # # Gallium Rubidium Oxygen Manganese Argon Carbon Silicon # @title "M\sD\N - current autocorrelation function" @xaxis label "Time (ps)" @yaxis label "< M\sD\N (0)\c7\CJ(t) > (e nm/ps)\S2" @TYPE xy # time M_D(0) J(t) acf Integral acf 0.000 -5.20584e-15 0 0.001 -6.97466e-15-1.42702e-17 0.002 -6.97511e-15-5.25081e-17 0.003 -6.97474e-15-9.07484e-17 0.004 -6.97391e-15-1.28987e-16 Why final value is infinity? If I do autocorrelation function of these values, I get all values 0. Why J(t)values are in range of e-15? Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] No default Ryckaert-Bell. types
I checked the line number in .top file. Its not reading any dihedral parameter defined in .itp file. NIlesh > > On 6/6/13 9:22 AM, Nilesh Dhumal wrote: >> Hello, >> >> I am getting "No default Ryckaert-Bell. types" error for grompp. >> >> I have define all this parameter in .itp file >> >> Here is .itp file >> >> ; For parameters see J. Phys. Chem. A. 2002, 106, 1074-1080 >> ; Derived from parsing of runfiles/alat.top.orig >> ;[ defaults ] >> ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ >> ;1 3 yes 0.5 0.5 >> ; comb-rule 3 is square-root sigma, the OPLSAA version >> >> [ atomtypes ] >> ; full atom descriptions are available in ffoplsaa.atp >> ; name bond_typemasscharge ptype sigma epsilon >> opls_124 S 1632.06000 0.312 A3.56000e-01 >> 1.65268e+00 opls_125 O 8 15.99940-0.556 A >> 2.93000e-01 1.17152e+00 opls_126 CT 6 15.03500-0.148 A >>3.81000e-01 6.69440e-01 opls_140 HC 1 1.00800 0.090 >> A2.5e-01 1.25520e-01 >> >> >> [ bondtypes ] >> ; ij func b0 kb >> S O 10.1530 225936.0 >> S CT 10.1800 100416.0 >> CTHC 10.1110 134724.8 >> >> >> [ angletypes ] >> ; ijk func th0 cth >>CT S CT 195.0 142.256 >>CT S O 1 106.75 330.536 >>S CT HC 1 111.3 192.8824 >>HC CT HC 1 108.4 148.532 >> >> >> [ dihedraltypes ] >> ; ijkl func coefficients >> ; OPLS Fourier dihedraltypes translated to Gromacs Ryckaert-Bellemans >> form >> ; according to the formula in the Gromacs manual. >> CT S CT HC 3 1.35352 4.06057 0.0 >> -5.41410 >> 0.0 0.0 ; sulfide all-atom >> O S CT HC 3 0.0 0.0 0.0 >> 0.0 >> 0.0 0.0 ; small ring >> >> >> >> Why I am getting this error. >> > > Apparently grompp is failing to find some needed parameter. You should > get a > line number in the topology where this is occurring, which will allow you > to map > back the atoms involved. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] No default Ryckaert-Bell. types
Hello, I am getting "No default Ryckaert-Bell. types" error for grompp. I have define all this parameter in .itp file Here is .itp file ; For parameters see J. Phys. Chem. A. 2002, 106, 1074-1080 ; Derived from parsing of runfiles/alat.top.orig ;[ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_124 S 1632.06000 0.312 A3.56000e-01 1.65268e+00 opls_125 O 8 15.99940-0.556 A 2.93000e-01 1.17152e+00 opls_126 CT 6 15.03500-0.148 A 3.81000e-01 6.69440e-01 opls_140 HC 1 1.00800 0.090 A2.5e-01 1.25520e-01 [ bondtypes ] ; ij func b0 kb S O 10.1530 225936.0 S CT 10.1800 100416.0 CTHC 10.1110 134724.8 [ angletypes ] ; ijk func th0 cth CT S CT 195.0 142.256 CT S O 1 106.75 330.536 S CT HC 1 111.3 192.8824 HC CT HC 1 108.4 148.532 [ dihedraltypes ] ; ijkl func coefficients ; OPLS Fourier dihedraltypes translated to Gromacs Ryckaert-Bellemans form ; according to the formula in the Gromacs manual. CT S CT HC 3 1.35352 4.06057 0.0 -5.41410 0.0 0.0 ; sulfide all-atom O S CT HC 3 0.0 0.0 0.0 0.0 0.0 0.0 ; small ring Why I am getting this error. I am using Gromacs VERSION 4.0.7. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Unknown bond_atomtype C2
Hello, I am getting "Unknown bond_atomtype C2" error for grompp. I don't have C2 atom in my .itp file. Here I used the .itp file ; For parameters see J. Phys. Chem. A. 2002, 106, 1074-1080 ; Derived from parsing of runfiles/alat.top.orig ;[ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_124 S 1632.06000 0.312 A3.56000e-01 1.65268e+00 opls_125 O 8 15.99940-0.556 A2.93000e-01 1.17152e+00 opls_126 CT 6 15.03500-0.148 A3.81000e-01 6.69440e-01 opls_140 HC 1 1.00800 0.090 A2.5e-01 1.25520e-01 [ bondtypes ] ; ij func b0 kb S O 10.1530 225936.0 S CT 10.1800 100416.0 CTHC 10.1110 134724.8 [ angletypes ] ; ijk func th0 cth CT S CT 195.0 142.256 CT S O 1 106.75 330.536 S CT HC 1 111.3 192.8824 HC CT HC 1 108.4 148.532 [ dihedraltypes ] ; ijkl func coefficients ; OPLS Fourier dihedraltypes translated to Gromacs Ryckaert-Bellemans form ; according to the formula in the Gromacs manual. CT S CT HC 3 1.35352 4.06057 0.0 -5.41410 0.0 0.0 ; sulfide all-atom O S CT HC 3 0.0 0.0 0.0 0.0 0.0 0.0 ; small ring I am not using atom C2 in my bonded parameters. Why I am getting this error. I am using Gromacs VERSION 4.0.7. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_hbond : autocorrelation funciton
-ac: average over all autocorrelations of the existence functions (either 0 or 1) of all hydrogen bonds. Program collect the data 0 or 1 along time? nilesh > On 4/14/13 7:21 PM, Nilesh Dhumal wrote: >> Hello, >> >> I am calculating the hyrogen bond life time my system using g_hbond in >> Gromacs. Program calculate the hydrogen bond life time from the >> autocorrelation function. Program calculate the hydrogen bond >> autocorrelation function with the hydrogen bond criteria. >> What quantity program use such as distance between donor-acceptor, to >> calculate the autocorrelation function? >> > > This is an adjustable option. Please read g_hbond -h. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_hbond : autocorrelation funciton
Hello, I am calculating the hyrogen bond life time my system using g_hbond in Gromacs. Program calculate the hydrogen bond life time from the autocorrelation function. Program calculate the hydrogen bond autocorrelation function with the hydrogen bond criteria. What quantity program use such as distance between donor-acceptor, to calculate the autocorrelation function? Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] autocorrelation function of hydrogen bond : g_hbond
Is oscillation is because of change in hydrogen bonded distance? Do program consider the change in hydrogen bonded distance during ACF calculation? Nilesh > There's a known oscillation in the ACF that occurs at ~100 fs or so. Is > that what you see? > > Erik > > On 9 Apr 2013, at 18:02, Nilesh Dhumal wrote: > >> >> >>> On Tue, Apr 9, 2013 at 11:47 AM, Nilesh Dhumal >>> wrote: >>> >>>> Hello, >>>> >>>> I am calculating the hydrogen bond autocorrelation function using >>>> g_hbond >>>> for O-H---O hydrogen bond in system. >>>> >>>> I made two groups 1. O-H atoms numbers 2. two oxygen atoms are >>>> interacting >>>> with OH bond. >>>> >>>> I am using default hydrogen bond criteria (donor-acceptor distance 3.5 >>>> and >>>> angle 30) for calculating the autocorrelation function. >>>> >>>> I am not getting a smooth exponential plot. I get a small bump in the >>>> plot. >>>> >>>> Attached the autocorrelation plot. >>>> >>>> >>> Attachments are not allowed on this list. Please provide a link to the >>> image. >>> >>> >>>> Why there is not smooth exponential plot. >>>> >>> >>> There is no way to tell, and even with the image there is still no way >>> to >>> tell. How much sampling do you have? Have you looked at overall >>> convergence, etc? >> >> >> I saved the trajectory at 3fs. >> >> It converged. >> >> Nilesh >> >> >> >> >>> >>> -Justin >>> >>> -- >>> >>> >>> >>> Justin A. Lemkul, Ph.D. >>> Research Scientist >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) >>> 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> >>> -- >>> gmx-users mailing listgmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >>> >> >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] autocorrelation function of hydrogen bond : g_hbond
> On Tue, Apr 9, 2013 at 11:47 AM, Nilesh Dhumal > wrote: > >> Hello, >> >> I am calculating the hydrogen bond autocorrelation function using >> g_hbond >> for O-H---O hydrogen bond in system. >> >> I made two groups 1. O-H atoms numbers 2. two oxygen atoms are >> interacting >> with OH bond. >> >> I am using default hydrogen bond criteria (donor-acceptor distance 3.5 >> and >> angle 30) for calculating the autocorrelation function. >> >> I am not getting a smooth exponential plot. I get a small bump in the >> plot. >> >> Attached the autocorrelation plot. >> >> > Attachments are not allowed on this list. Please provide a link to the > image. > > >> Why there is not smooth exponential plot. >> > > There is no way to tell, and even with the image there is still no way to > tell. How much sampling do you have? Have you looked at overall > convergence, etc? I saved the trajectory at 3fs. It converged. Nilesh > > -Justin > > -- > > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) > 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] autocorrelation function of hydrogen bond : g_hbond
Hello, I am calculating the hydrogen bond autocorrelation function using g_hbond for O-H---O hydrogen bond in system. I made two groups 1. O-H atoms numbers 2. two oxygen atoms are interacting with OH bond. I am using default hydrogen bond criteria (donor-acceptor distance 3.5 and angle 30) for calculating the autocorrelation function. I am not getting a smooth exponential plot. I get a small bump in the plot. Attached the autocorrelation plot. Why there is not smooth exponential plot. Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_hbond
Hello, I am calculating the hydrogen bond life time for my system, ionic liquids. I am calculating the hydrogen bond life time using g_hbond in Groamcs. Attached the plot p(t)vs time and the exponential decay is not sooth. Can you tell why is there is lot of noise. Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_hbond
Hello, I am calculating the hydrogen bond life time for my system. Do program consider the hydrogen bond criteria for calculation of autocorrelation function? Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: AW: AW: AW: AW: AW: AW: AW: [gmx-users] g_current
Hello, I run a 500ps simulation and save the trajectory each 3fs. g_current work till 498ps and later it shows -nan. Can you tell where is the problem Nilesh > Hi, > Now I've tested the version of g_current in 4.6 and for me it works fine. > /Flo > >> -Ursprüngliche Nachricht- >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> boun...@gromacs.org] Im Auftrag von Florian Dommert >> Gesendet: Mittwoch, 27. Februar 2013 18:46 >> An: 'Discussion list for GROMACS users' >> Betreff: AW: AW: AW: AW: AW: AW: AW: [gmx-users] g_current >> >> > -Ursprüngliche Nachricht- >> > Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> > boun...@gromacs.org] Im Auftrag von Nilesh Dhumal >> > Gesendet: Mittwoch, 27. Februar 2013 17:38 >> > An: Discussion list for GROMACS users >> > Betreff: Re: AW: AW: AW: AW: AW: AW: [gmx-users] g_current >> > >> > Hello, >> > >> > I am using g_current for first time. Now I am running additional >> simulation and I >> > will save trajectory at 2 fs. >> > >> > Is it possible to calculate contribution of rotational and translation to >> dipole >> > moment simultaneously with the simulation instead of saving the trajectory >> at >> > each 2fs? >> > >> >> Hi, >> >> This is one of my majors on my to do list, but currently not possible. >> I > think a >> saving frequency of 0.05 ps should be fine. >> >> /Flo >> >> >> > Nilesh >> > >> > > Hi, >> > > >> > > Have you done a similar analysis with another IL system or is it >> > > the first time you use g_current? Currently I am not able to figure out what the problem is. However 2ps saving interval is quite long for such a kind of analysis. A zero value of the translational dipole moment hints to neutral molecules which should not be the case for your system. What is written in the output of mj.xvg. Is filled with zeros? >> > > >> > > /Flo >> > > >> > > >> > >> -Ursprüngliche Nachricht- >> > >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> > >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal >> > >> Gesendet: Mittwoch, 27. Februar 2013 15:26 >> > >> An: Discussion list for GROMACS users >> > >> Betreff: Re: AW: AW: AW: AW: AW: [gmx-users] g_current >> > >> >> > >> Hello, >> > >> >> > >> Yes. Segfault is solved. I saving velocites and coordinates at 2 >> ps. >> > >> >> > >> Nilesh >> > >> >> > >> > Hi, >> > >> > >> > >> > At least the segfault is solved. However, the zero output of M_J >> > >> > for your IL system is really strange. I'm thinking about a reason, but I am currently not able to find one. How often do you write out velocities and coordinates in your trr file? >> > >> > >> > >> > /Flo >> > >> > >> > >> >> -Ursprüngliche Nachricht- >> > >> >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> > >> >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal >> > >> >> Gesendet: Dienstag, 26. Februar 2013 17:50 >> > >> >> An: Discussion list for GROMACS users >> > >> >> Betreff: Re: AW: AW: AW: AW: [gmx-users] g_current >> > >> >> >> > >> >> Hello, >> > >> >> >> > >> >> I didn't get any segmental fault if I use Gromacs Version 4.5.5. >> > >> >> >> > >> >> g_current -f md.trr -s md.tpr -mc >> > >> >> >> > >> >> Program didn't write the mc.xvg >> > >> >> >> > >> >> Average translational dipole moment is zero. >> > >> >> >> > >> >> Average translational dipole moment M_J [enm] after 15001 frames (|M|^2): >> > >> >> -0.00 -0.00 -0.00 (0.00) >> > >> >> >> > >> >> Can you tell where is the problem? >> > >> >> >> > >> >> Nilesh >> > >> >> >> > >> >> > Hi, >> > >> >> > I am using the release branch of 4.5. >> > >> >> > >> > >> >> > /Flo >>
Re: AW: AW: AW: AW: AW: AW: AW: [gmx-users] g_current
Hello, I run a 500ps simulation and save the trajectory each 3fs. g_current work till 498ps and later it shows -nan. Can you tell where is the problem Nilesh > Hi, > Now I've tested the version of g_current in 4.6 and for me it works fine. > /Flo > >> -Ursprüngliche Nachricht- >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> boun...@gromacs.org] Im Auftrag von Florian Dommert >> Gesendet: Mittwoch, 27. Februar 2013 18:46 >> An: 'Discussion list for GROMACS users' >> Betreff: AW: AW: AW: AW: AW: AW: AW: [gmx-users] g_current >> >> > -Ursprüngliche Nachricht- >> > Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> > boun...@gromacs.org] Im Auftrag von Nilesh Dhumal >> > Gesendet: Mittwoch, 27. Februar 2013 17:38 >> > An: Discussion list for GROMACS users >> > Betreff: Re: AW: AW: AW: AW: AW: AW: [gmx-users] g_current >> > >> > Hello, >> > >> > I am using g_current for first time. Now I am running additional >> simulation and I >> > will save trajectory at 2 fs. >> > >> > Is it possible to calculate contribution of rotational and translation >> > to >> dipole >> > moment simultaneously with the simulation instead of saving the >> > trajectory >> at >> > each 2fs? >> > >> >> Hi, >> >> This is one of my majors on my to do list, but currently not possible. >> I > think a >> saving frequency of 0.05 ps should be fine. >> >> /Flo >> >> >> > Nilesh >> > >> > > Hi, >> > > >> > > Have you done a similar analysis with another IL system or is it >> > > the first time you use g_current? Currently I am not able to figure >> > > out what the problem is. However 2ps saving interval is quite long >> > > for such a kind of analysis. A zero value of the translational >> > > dipole moment hints to neutral molecules which should not be the >> > > case for your system. What is written in the output of mj.xvg. Is >> > > filled with zeros? >> > > >> > > /Flo >> > > >> > > >> > >> -Ursprüngliche Nachricht- >> > >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> > >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal >> > >> Gesendet: Mittwoch, 27. Februar 2013 15:26 >> > >> An: Discussion list for GROMACS users >> > >> Betreff: Re: AW: AW: AW: AW: AW: [gmx-users] g_current >> > >> >> > >> Hello, >> > >> >> > >> Yes. Segfault is solved. I saving velocites and coordinates at 2 >> ps. >> > >> >> > >> Nilesh >> > >> >> > >> > Hi, >> > >> > >> > >> > At least the segfault is solved. However, the zero output of M_J >> > >> > for your IL system is really strange. I'm thinking about a >> > >> > reason, but I am currently not able to find one. How often do you >> > >> > write out velocities and coordinates in your trr file? >> > >> > >> > >> > /Flo >> > >> > >> > >> >> -Ursprüngliche Nachricht- >> > >> >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> > >> >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal >> > >> >> Gesendet: Dienstag, 26. Februar 2013 17:50 >> > >> >> An: Discussion list for GROMACS users >> > >> >> Betreff: Re: AW: AW: AW: AW: [gmx-users] g_current >> > >> >> >> > >> >> Hello, >> > >> >> >> > >> >> I didn't get any segmental fault if I use Gromacs Version 4.5.5. >> > >> >> >> > >> >> g_current -f md.trr -s md.tpr -mc >> > >> >> >> > >> >> Program didn't write the mc.xvg >> > >> >> >> > >> >> Average translational dipole moment is zero. >> > >> >> >> > >> >> Average translational dipole moment M_J [enm] after 15001 frames >> > >> >> (|M|^2): >> > >> >> -0.00 -0.00 -0.00 (0.00) >> > >> >> >> > >> >> Can you tell where is the problem? >> > >> >> >> > >> >> Nilesh
Re: AW: AW: AW: AW: AW: AW: [gmx-users] g_current
Hello, I am using g_current for first time. Now I am running additional simulation and I will save trajectory at 2 fs. Is it possible to calculate contribution of rotational and translation to dipole moment simultaneously with the simulation instead of saving the trajectory at each 2fs? Nilesh > Hi, > > Have you done a similar analysis with another IL system or is it the > first > time you use g_current? Currently I am not able to figure out what the > problem is. However 2ps saving interval is quite long for such a kind of > analysis. A zero value of the translational dipole moment hints to neutral > molecules which should not be the case for your system. What is written in > the output of mj.xvg. Is filled with zeros? > > /Flo > > >> -Ursprüngliche Nachricht- >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal >> Gesendet: Mittwoch, 27. Februar 2013 15:26 >> An: Discussion list for GROMACS users >> Betreff: Re: AW: AW: AW: AW: AW: [gmx-users] g_current >> >> Hello, >> >> Yes. Segfault is solved. I saving velocites and coordinates at 2 ps. >> >> Nilesh >> >> > Hi, >> > >> > At least the segfault is solved. However, the zero output of M_J for >> > your IL system is really strange. I'm thinking about a reason, but I >> > am currently not able to find one. How often do you write out >> > velocities and coordinates in your trr file? >> > >> > /Flo >> > >> >> -Ursprüngliche Nachricht- >> >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal >> >> Gesendet: Dienstag, 26. Februar 2013 17:50 >> >> An: Discussion list for GROMACS users >> >> Betreff: Re: AW: AW: AW: AW: [gmx-users] g_current >> >> >> >> Hello, >> >> >> >> I didn't get any segmental fault if I use Gromacs Version 4.5.5. >> >> >> >> g_current -f md.trr -s md.tpr -mc >> >> >> >> Program didn't write the mc.xvg >> >> >> >> Average translational dipole moment is zero. >> >> >> >> Average translational dipole moment M_J [enm] after 15001 frames >> >> (|M|^2): >> >> -0.00 -0.00 -0.00 (0.00) >> >> >> >> Can you tell where is the problem? >> >> >> >> Nilesh >> >> >> >> > Hi, >> >> > I am using the release branch of 4.5. >> >> > >> >> > /Flo >> >> > >> >> > --- >> >> > Florian Dommert >> >> > Dipl. Phys. >> >> > >> >> > Institut für Computerphysik >> >> > Universität Stuttgart >> >> > Allmandring 3 >> >> > D-70569 Stuttgart >> >> > >> >> > Tel.: 0711-68563613 >> >> > Fax: 0711-68563658 >> >> > >> >> > >> >> >> -Ursprüngliche Nachricht- >> >> >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> >> >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal >> >> >> Gesendet: Montag, 25. Februar 2013 15:35 >> >> >> An: Discussion list for GROMACS users >> >> >> Betreff: Re: AW: AW: AW: [gmx-users] g_current >> >> >> >> >> >> Hello, >> >> >> >> >> >> Thanks. >> >> >> >> >> >> I will update Gromacs version. Can you tell which version you are >> >> >> using ? >> >> >> >> >> >> Nilesh >> >> >> >> >> >> > Hi, >> >> >> > >> >> >> > Can you update your Gromacs version to an actual release and >> >> >> > check if the problem still occurs. It is very strange that the >> >> >> > Einstein-Helfand fit gives >> >> >> > 0 for sigma and M_J^2. >> >> >> > >> >> >> > Cheers, >> >> >> > Flo >> >> >> > >> >> >> > --- >> >> >> > Florian Dommert >> >> >> > Dipl. Phys. >> >> >> > >> >> >> > Institut für Computerphysik >> >> >> > Universität Stuttgart >> >> >> > Allmandring 3 >> >> >> > D-7
Re: AW: AW: AW: AW: AW: [gmx-users] g_current
Hello, Yes. Segfault is solved. I saving velocites and coordinates at 2 ps. Nilesh > Hi, > > At least the segfault is solved. However, the zero output of M_J for your > IL system is really strange. I'm thinking about a reason, but I am > currently > not able to find one. How often do you write out velocities and > coordinates > in your trr file? > > /Flo > >> -Ursprüngliche Nachricht- >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal >> Gesendet: Dienstag, 26. Februar 2013 17:50 >> An: Discussion list for GROMACS users >> Betreff: Re: AW: AW: AW: AW: [gmx-users] g_current >> >> Hello, >> >> I didn't get any segmental fault if I use Gromacs Version 4.5.5. >> >> g_current -f md.trr -s md.tpr -mc >> >> Program didn't write the mc.xvg >> >> Average translational dipole moment is zero. >> >> Average translational dipole moment M_J [enm] after 15001 frames >> (|M|^2): >> -0.00 -0.00 -0.00 (0.00) >> >> Can you tell where is the problem? >> >> Nilesh >> >> > Hi, >> > I am using the release branch of 4.5. >> > >> > /Flo >> > >> > --- >> > Florian Dommert >> > Dipl. Phys. >> > >> > Institut für Computerphysik >> > Universität Stuttgart >> > Allmandring 3 >> > D-70569 Stuttgart >> > >> > Tel.: 0711-68563613 >> > Fax: 0711-68563658 >> > >> > >> >> -Ursprüngliche Nachricht- >> >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal >> >> Gesendet: Montag, 25. Februar 2013 15:35 >> >> An: Discussion list for GROMACS users >> >> Betreff: Re: AW: AW: AW: [gmx-users] g_current >> >> >> >> Hello, >> >> >> >> Thanks. >> >> >> >> I will update Gromacs version. Can you tell which version you are >> >> using ? >> >> >> >> Nilesh >> >> >> >> > Hi, >> >> > >> >> > Can you update your Gromacs version to an actual release and check >> >> > if the problem still occurs. It is very strange that the >> >> > Einstein-Helfand fit gives >> >> > 0 for sigma and M_J^2. >> >> > >> >> > Cheers, >> >> > Flo >> >> > >> >> > --- >> >> > Florian Dommert >> >> > Dipl. Phys. >> >> > >> >> > Institut für Computerphysik >> >> > Universität Stuttgart >> >> > Allmandring 3 >> >> > D-70569 Stuttgart >> >> > >> >> > Tel.: 0711-68563613 >> >> > Fax: 0711-68563658 >> >> > >> >> >> -Ursprüngliche Nachricht- >> >> >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> >> >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal >> >> >> Gesendet: Montag, 25. Februar 2013 14:00 >> >> >> An: Discussion list for GROMACS users >> >> >> Betreff: Re: AW: AW: [gmx-users] g_current >> >> >> >> >> >> Hello, >> >> >> >> >> >> I am using Gromacs VERSION 4.0.7. >> >> >> >> >> >> Nilesh >> >> >> >> >> >> >> >> >> > Hi, >> >> >> > >> >> >> > Which version of gromacs are you using. I am applying this tool >> >> >> > also to ILs and it works fine for me in the release-4-5 branch. >> >> >> > It is especially strange that you have a rotational dipole >> >> >> > moment of >> > zero. >> >> >> > However, currently I have no idea where the segfault arises. >> >> >> > Especially because you get an output. >> >> >> > So >> >> >> > what version you are using? >> >> >> > >> >> >> > Cheers, >> >> >> > Flo >> >> >> > >> >> >> >> -Ursprüngliche Nachricht- >> >> >> >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> >> >> >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal >> >> >> >> Gesen
Re: AW: AW: AW: AW: [gmx-users] g_current
Hello, I didn't get any segmental fault if I use Gromacs Version 4.5.5. g_current -f md.trr -s md.tpr -mc Program didn't write the mc.xvg Average translational dipole moment is zero. Average translational dipole moment M_J [enm] after 15001 frames (|M|^2): -0.00 -0.00 -0.00 (0.00) Can you tell where is the problem? Nilesh > Hi, > I am using the release branch of 4.5. > > /Flo > > --- > Florian Dommert > Dipl. Phys. > > Institut für Computerphysik > Universität Stuttgart > Allmandring 3 > D-70569 Stuttgart > > Tel.: 0711-68563613 > Fax: 0711-68563658 > > >> -Ursprüngliche Nachricht- >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal >> Gesendet: Montag, 25. Februar 2013 15:35 >> An: Discussion list for GROMACS users >> Betreff: Re: AW: AW: AW: [gmx-users] g_current >> >> Hello, >> >> Thanks. >> >> I will update Gromacs version. Can you tell which version you are using >> ? >> >> Nilesh >> >> > Hi, >> > >> > Can you update your Gromacs version to an actual release and check if >> > the problem still occurs. It is very strange that the Einstein-Helfand >> > fit gives >> > 0 for sigma and M_J^2. >> > >> > Cheers, >> > Flo >> > >> > --- >> > Florian Dommert >> > Dipl. Phys. >> > >> > Institut für Computerphysik >> > Universität Stuttgart >> > Allmandring 3 >> > D-70569 Stuttgart >> > >> > Tel.: 0711-68563613 >> > Fax: 0711-68563658 >> > >> >> -Ursprüngliche Nachricht- >> >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal >> >> Gesendet: Montag, 25. Februar 2013 14:00 >> >> An: Discussion list for GROMACS users >> >> Betreff: Re: AW: AW: [gmx-users] g_current >> >> >> >> Hello, >> >> >> >> I am using Gromacs VERSION 4.0.7. >> >> >> >> Nilesh >> >> >> >> >> >> > Hi, >> >> > >> >> > Which version of gromacs are you using. I am applying this tool >> >> > also to ILs and it works fine for me in the release-4-5 branch. It >> >> > is especially strange that you have a rotational dipole moment of > zero. >> >> > However, currently I have no idea where the segfault arises. >> >> > Especially because you get an output. >> >> > So >> >> > what version you are using? >> >> > >> >> > Cheers, >> >> > Flo >> >> > >> >> >> -Ursprüngliche Nachricht- >> >> >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> >> >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal >> >> >> Gesendet: Montag, 25. Februar 2013 00:05 >> >> >> An: Discussion list for GROMACS users >> >> >> Betreff: Re: AW: [gmx-users] g_current >> >> >> >> >> >> Hello, >> >> >> >> >> >> My system is ionic liquids composed of 128 cation (EMIM) and 128 >> >> >> anion >> >> > (ethyl >> >> >> sulfate). I choose system (0) as index group. >> >> >> >> >> >> Nilesh >> >> >> >> >> >> > Hi, >> >> >> > >> >> >> > Can you be a little bit more specific about your system, and >> >> >> > what you have chosen as index groups ? >> >> >> > >> >> >> > /Flo >> >> >> > >> >> >> > --- >> >> >> > Florian Dommert >> >> >> > Dipl. Phys. >> >> >> > >> >> >> > Institut für Computerphysik >> >> >> > Universität Stuttgart >> >> >> > Allmandring 3 >> >> >> > D-70569 Stuttgart >> >> >> > >> >> >> > Tel.: 0711-68563613 >> >> >> > Fax: 0711-68563658 >> >> >> > >> >> >> >> -Ursprüngliche Nachricht- >> >> >> >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> >> >> >> boun...@gromacs.org]
Re: AW: AW: AW: [gmx-users] g_current
Hello, Thanks. I will update Gromacs version. Can you tell which version you are using ? Nilesh > Hi, > > Can you update your Gromacs version to an actual release and check if the > problem still occurs. It is very strange that the Einstein-Helfand fit > gives > 0 for sigma and M_J^2. > > Cheers, > Flo > > --- > Florian Dommert > Dipl. Phys. > > Institut für Computerphysik > Universität Stuttgart > Allmandring 3 > D-70569 Stuttgart > > Tel.: 0711-68563613 > Fax: 0711-68563658 > >> -Ursprüngliche Nachricht- >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal >> Gesendet: Montag, 25. Februar 2013 14:00 >> An: Discussion list for GROMACS users >> Betreff: Re: AW: AW: [gmx-users] g_current >> >> Hello, >> >> I am using Gromacs VERSION 4.0.7. >> >> Nilesh >> >> >> > Hi, >> > >> > Which version of gromacs are you using. I am applying this tool also >> > to ILs and it works fine for me in the release-4-5 branch. It is >> > especially strange that you have a rotational dipole moment of zero. >> > However, currently I have no idea where the segfault arises. >> > Especially because you get an output. >> > So >> > what version you are using? >> > >> > Cheers, >> > Flo >> > >> >> -Ursprüngliche Nachricht- >> >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal >> >> Gesendet: Montag, 25. Februar 2013 00:05 >> >> An: Discussion list for GROMACS users >> >> Betreff: Re: AW: [gmx-users] g_current >> >> >> >> Hello, >> >> >> >> My system is ionic liquids composed of 128 cation (EMIM) and 128 >> >> anion >> > (ethyl >> >> sulfate). I choose system (0) as index group. >> >> >> >> Nilesh >> >> >> >> > Hi, >> >> > >> >> > Can you be a little bit more specific about your system, and what >> >> > you have chosen as index groups ? >> >> > >> >> > /Flo >> >> > >> >> > --- >> >> > Florian Dommert >> >> > Dipl. Phys. >> >> > >> >> > Institut für Computerphysik >> >> > Universität Stuttgart >> >> > Allmandring 3 >> >> > D-70569 Stuttgart >> >> > >> >> > Tel.: 0711-68563613 >> >> > Fax: 0711-68563658 >> >> > >> >> >> -Ursprüngliche Nachricht- >> >> >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> >> >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal >> >> >> Gesendet: Samstag, 23. Februar 2013 16:17 >> >> >> An: gmx-users@gromacs.org >> >> >> Betreff: [gmx-users] g_current >> >> >> >> >> >> Hello, >> >> >> >> >> >> I am calculating the correlation of the rotational and >> >> >> translational >> >> > dipole >> >> >> moment of the system using g_current. >> >> >> >> >> >> I used following command >> >> >> >> >> >> g_current -f md.trr -s md.tpr mc >> >> >> >> >> >> It crashed with segmental fault. >> >> >> Last frame 15000 time 3.002 >> >> >> Prefactor fit E-H: 1 / 6.0*V*k_B*T: 2.45747e-11 >> >> >> >> >> >> >> >> >> Average translational dipole moment M_J [enm] after 15001 frames >> >> >> (|M|^2): >> >> >> -0.00 -0.00 -0.00 (0.00) >> >> >> >> >> >> >> >> >> Average molecular dipole moment M_D [enm] after 15001 frames >> (|M|^2): >> >> >> -7.281919 17.954138 5.845435 (490.493744) >> >> >> >> >> >> >> >> >> >> >> >> Absolute values: >> >> >> epsilon=2723.718750 >> >> >> , , <(M_J*M_D)^2>: (490.493744, 0.00, >> >> >> -0.03) >> >> >> >> >> >> >> >> >> >> >> >> >>
Re: AW: AW: [gmx-users] g_current
Hello, I am using Gromacs VERSION 4.0.7. Nilesh > Hi, > > Which version of gromacs are you using. I am applying this tool also to > ILs > and it works fine for me in the release-4-5 branch. It is especially > strange > that you have a rotational dipole moment of zero. However, currently I > have > no idea where the segfault arises. Especially because you get an output. > So > what version you are using? > > Cheers, > Flo > >> -Ursprüngliche Nachricht- >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal >> Gesendet: Montag, 25. Februar 2013 00:05 >> An: Discussion list for GROMACS users >> Betreff: Re: AW: [gmx-users] g_current >> >> Hello, >> >> My system is ionic liquids composed of 128 cation (EMIM) and 128 anion > (ethyl >> sulfate). I choose system (0) as index group. >> >> Nilesh >> >> > Hi, >> > >> > Can you be a little bit more specific about your system, and what you >> > have chosen as index groups ? >> > >> > /Flo >> > >> > --- >> > Florian Dommert >> > Dipl. Phys. >> > >> > Institut für Computerphysik >> > Universität Stuttgart >> > Allmandring 3 >> > D-70569 Stuttgart >> > >> > Tel.: 0711-68563613 >> > Fax: 0711-68563658 >> > >> >> -Ursprüngliche Nachricht- >> >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal >> >> Gesendet: Samstag, 23. Februar 2013 16:17 >> >> An: gmx-users@gromacs.org >> >> Betreff: [gmx-users] g_current >> >> >> >> Hello, >> >> >> >> I am calculating the correlation of the rotational and translational >> > dipole >> >> moment of the system using g_current. >> >> >> >> I used following command >> >> >> >> g_current -f md.trr -s md.tpr mc >> >> >> >> It crashed with segmental fault. >> >> Last frame 15000 time 3.002 >> >> Prefactor fit E-H: 1 / 6.0*V*k_B*T: 2.45747e-11 >> >> >> >> >> >> Average translational dipole moment M_J [enm] after 15001 frames >> >> (|M|^2): >> >> -0.00 -0.00 -0.00 (0.00) >> >> >> >> >> >> Average molecular dipole moment M_D [enm] after 15001 frames (|M|^2): >> >> -7.281919 17.954138 5.845435 (490.493744) >> >> >> >> >> >> >> >> Absolute values: >> >> epsilon=2723.718750 >> >> , , <(M_J*M_D)^2>: (490.493744, 0.00, -0.03) >> >> >> >> >> >> >> >> >> >> Fluctuations: >> >> epsilon=450.336090 >> >> >> >> >> >> deltaM_D , deltaM_J, deltaM_JD: (80.947235, 0.00, 0.00) >> >> >> >> >> >> >> >> Static dielectric constant using integral and fluctuations: >> >> 450.336090 >> >> >> >> < M_JM_D > via integral: -0.000 >> >> >> >> *** >> >> >> >> Average volume V=42.031509 nm^3 at T=300.00 K and corresponding >> >> refactor 1.0 / 3.0*V*k_B*T*EPSILON_0: 5.550975 >> >> >> >> Start fit at 98.08 ps (100.00). >> >> End fit at 398.31 ps (400.00). >> >> >> >> Einstein-Helfand fit to the MSD of the translational dipole moment >> >> yields: >> >> >> >> sigma=0. >> >> translational fraction of M^2: 0. Dielectric constant using EH: >> >> 2723.7188 Segmentation fault >> >> >> >> >> >> Can you whats the problem? >> >> >> >> Nilesh >> >> >> >> -- >> >> gmx-users mailing listgmx-users@gromacs.org >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> >> * Please search the archive at >> >> http://www.gromacs.org/Support/Mailing_Lists/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
Re: AW: [gmx-users] g_current
Hello, My system is ionic liquids composed of 128 cation (EMIM) and 128 anion (ethyl sulfate). I choose system (0) as index group. Nilesh > Hi, > > Can you be a little bit more specific about your system, and what you > have > chosen as index groups ? > > /Flo > > --- > Florian Dommert > Dipl. Phys. > > Institut für Computerphysik > Universität Stuttgart > Allmandring 3 > D-70569 Stuttgart > > Tel.: 0711-68563613 > Fax: 0711-68563658 > >> -Ursprüngliche Nachricht- >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal >> Gesendet: Samstag, 23. Februar 2013 16:17 >> An: gmx-users@gromacs.org >> Betreff: [gmx-users] g_current >> >> Hello, >> >> I am calculating the correlation of the rotational and translational > dipole >> moment of the system using g_current. >> >> I used following command >> >> g_current -f md.trr -s md.tpr mc >> >> It crashed with segmental fault. >> Last frame 15000 time 3.002 >> Prefactor fit E-H: 1 / 6.0*V*k_B*T: 2.45747e-11 >> >> >> Average translational dipole moment M_J [enm] after 15001 frames >> (|M|^2): >> -0.00 -0.00 -0.00 (0.00) >> >> >> Average molecular dipole moment M_D [enm] after 15001 frames (|M|^2): >> -7.281919 17.954138 5.845435 (490.493744) >> >> >> >> Absolute values: >> epsilon=2723.718750 >> , , <(M_J*M_D)^2>: (490.493744, 0.00, -0.03) >> >> >> >> >> Fluctuations: >> epsilon=450.336090 >> >> >> deltaM_D , deltaM_J, deltaM_JD: (80.947235, 0.00, 0.00) >> >> >> >> Static dielectric constant using integral and fluctuations: 450.336090 >> >> < M_JM_D > via integral: -0.000 >> >> *** >> >> Average volume V=42.031509 nm^3 at T=300.00 K and corresponding >> refactor 1.0 / 3.0*V*k_B*T*EPSILON_0: 5.550975 >> >> Start fit at 98.08 ps (100.00). >> End fit at 398.31 ps (400.00). >> >> Einstein-Helfand fit to the MSD of the translational dipole moment >> yields: >> >> sigma=0. >> translational fraction of M^2: 0. >> Dielectric constant using EH: 2723.7188 >> Segmentation fault >> >> >> Can you whats the problem? >> >> Nilesh >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_current
Hello, I am calculating the correlation of the rotational and translational dipole moment of the system using g_current. I used following command g_current -f md.trr -s md.tpr mc It crashed with segmental fault. Last frame 15000 time 3.002 Prefactor fit E-H: 1 / 6.0*V*k_B*T: 2.45747e-11 Average translational dipole moment M_J [enm] after 15001 frames (|M|^2): -0.00 -0.00 -0.00 (0.00) Average molecular dipole moment M_D [enm] after 15001 frames (|M|^2): -7.281919 17.954138 5.845435 (490.493744) Absolute values: epsilon=2723.718750 , , <(M_J*M_D)^2>: (490.493744, 0.00, -0.03) Fluctuations: epsilon=450.336090 deltaM_D , deltaM_J, deltaM_JD: (80.947235, 0.00, 0.00) Static dielectric constant using integral and fluctuations: 450.336090 < M_JM_D > via integral: -0.000 *** Average volume V=42.031509 nm^3 at T=300.00 K and corresponding refactor 1.0 / 3.0*V*k_B*T*EPSILON_0: 5.550975 Start fit at 98.08 ps (100.00). End fit at 398.31 ps (400.00). Einstein-Helfand fit to the MSD of the translational dipole moment yields: sigma=0. translational fraction of M^2: 0. Dielectric constant using EH: 2723.7188 Segmentation fault Can you whats the problem? Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Dipole moment
Is it possible to calcualte the dipole moment at 3fs by modifing the source code? Nilesh > How can I save the total dipole moment extacted by .edr file? > > I could not find the option in g_energy. > > Nilesh > > >> Justin is right. I've slipped a bit, that was not the way to set >> nstenergy. But still, you can save the dipole directly in the edr file. >> Not from your existing trajectory, but in a new run. Say your dt=1fs, >> then you should set nstenergy=3 to get your dipole moment every 3fs >> which you can retrieve with g_energy. >> >> Javier >> >> >> El 18/10/12 20:43, Nilesh Dhumal escribió: >>> In short, I can not save dipole moment directly. I can calculate dipole >>> moment only using .trr file. >>> >>> Nilesh >>>> On 10/18/12 1:45 PM, Javier Cerezo wrote: >>>>> Hi >>>>> >>>>> The dipole is stored in the edr file, which output frequency is >>>>> controlled by >>>>> "nstenergy" option in the mdp parameter file. Set it appropriately >>>>> during your >>>>> run (nstenergy=0.003) but keep in mind that it should be a multiple >>>>> of >>>>> the time >>>>> step. >>>>> >>>> nstenergy cannot be set this way; it is an integer indicating the >>>> interval >>>> (in >>>> number of steps) for writing energy values. If the values have been >>>> saved >>>> every >>>> 2 ps, there is no way to retrieve them every 3 fs; if more frequent >>>> information >>>> is needed, it needs to be saved more frequently. >>>> >>>> -Justin >>>> >>>>> El 18/10/12 18:09, Nilesh Dhumal escribió: >>>>>> Hello, >>>>>> >>>>>> I am calculating the dipole moment auto-correlation function for my >>>>>> system >>>>>> which have 128 cation and 128 anion. >>>>>> >>>>>> I am saving the trajectory at each 2 ps and using this trajectory >>>>>> for >>>>>> further analysis. >>>>>> >>>>>> Can I save the dipole moment and three vectors at each 3 fs? >>>>>> >>>>>> >>>>>> >>>>>> Thanks >>>>>> >>>>>> Nilesh >>>>>> >>>>>> >>>>>> >>>>>> >>>> -- >>>> >>>> >>>> Justin A. Lemkul, Ph.D. >>>> Research Scientist >>>> Department of Biochemistry >>>> Virginia Tech >>>> Blacksburg, VA >>>> jalemkul[at]vt.edu | (540) 231-9080 >>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>>> >>>> >>>> -- >>>> gmx-users mailing listgmx-users@gromacs.org >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >>>> >>>> >>> >> >> -- >> Javier CEREZO BASTIDA >> Ph.D. Student >> Physical Chemistry >> Universidad de Murcia >> 30100, Murcia (SPAIN) >> T: (0034)868887434 >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >> >> > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Dipole moment
How can I save the total dipole moment extacted by .edr file? I could not find the option in g_energy. Nilesh > Justin is right. I've slipped a bit, that was not the way to set > nstenergy. But still, you can save the dipole directly in the edr file. > Not from your existing trajectory, but in a new run. Say your dt=1fs, > then you should set nstenergy=3 to get your dipole moment every 3fs > which you can retrieve with g_energy. > > Javier > > > El 18/10/12 20:43, Nilesh Dhumal escribió: >> In short, I can not save dipole moment directly. I can calculate dipole >> moment only using .trr file. >> >> Nilesh >>> On 10/18/12 1:45 PM, Javier Cerezo wrote: >>>> Hi >>>> >>>> The dipole is stored in the edr file, which output frequency is >>>> controlled by >>>> "nstenergy" option in the mdp parameter file. Set it appropriately >>>> during your >>>> run (nstenergy=0.003) but keep in mind that it should be a multiple of >>>> the time >>>> step. >>>> >>> nstenergy cannot be set this way; it is an integer indicating the >>> interval >>> (in >>> number of steps) for writing energy values. If the values have been >>> saved >>> every >>> 2 ps, there is no way to retrieve them every 3 fs; if more frequent >>> information >>> is needed, it needs to be saved more frequently. >>> >>> -Justin >>> >>>> El 18/10/12 18:09, Nilesh Dhumal escribió: >>>>> Hello, >>>>> >>>>> I am calculating the dipole moment auto-correlation function for my >>>>> system >>>>> which have 128 cation and 128 anion. >>>>> >>>>> I am saving the trajectory at each 2 ps and using this trajectory for >>>>> further analysis. >>>>> >>>>> Can I save the dipole moment and three vectors at each 3 fs? >>>>> >>>>> >>>>> >>>>> Thanks >>>>> >>>>> Nilesh >>>>> >>>>> >>>>> >>>>> >>> -- >>> >>> >>> Justin A. Lemkul, Ph.D. >>> Research Scientist >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> >>> -- >>> gmx-users mailing listgmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >>> >>> >> > > -- > Javier CEREZO BASTIDA > Ph.D. Student > Physical Chemistry > Universidad de Murcia > 30100, Murcia (SPAIN) > T: (0034)868887434 > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Dipole moment
In short, I can not save dipole moment directly. I can calculate dipole moment only using .trr file. Nilesh > > On 10/18/12 1:45 PM, Javier Cerezo wrote: >> Hi >> >> The dipole is stored in the edr file, which output frequency is >> controlled by >> "nstenergy" option in the mdp parameter file. Set it appropriately >> during your >> run (nstenergy=0.003) but keep in mind that it should be a multiple of >> the time >> step. >> > > nstenergy cannot be set this way; it is an integer indicating the interval > (in > number of steps) for writing energy values. If the values have been saved > every > 2 ps, there is no way to retrieve them every 3 fs; if more frequent > information > is needed, it needs to be saved more frequently. > > -Justin > >> >> El 18/10/12 18:09, Nilesh Dhumal escribió: >>> Hello, >>> >>> I am calculating the dipole moment auto-correlation function for my >>> system >>> which have 128 cation and 128 anion. >>> >>> I am saving the trajectory at each 2 ps and using this trajectory for >>> further analysis. >>> >>> Can I save the dipole moment and three vectors at each 3 fs? >>> >>> >>> >>> Thanks >>> >>> Nilesh >>> >>> >>> >>> >> > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Dipole moment
In short, I can save dipole moment with the same frequency, the trajectory save. Nilesh > > On 10/18/12 1:45 PM, Javier Cerezo wrote: >> Hi >> >> The dipole is stored in the edr file, which output frequency is >> controlled by >> "nstenergy" option in the mdp parameter file. Set it appropriately >> during your >> run (nstenergy=0.003) but keep in mind that it should be a multiple of >> the time >> step. >> > > nstenergy cannot be set this way; it is an integer indicating the interval > (in > number of steps) for writing energy values. If the values have been saved > every > 2 ps, there is no way to retrieve them every 3 fs; if more frequent > information > is needed, it needs to be saved more frequently. > > -Justin > >> >> El 18/10/12 18:09, Nilesh Dhumal escribió: >>> Hello, >>> >>> I am calculating the dipole moment auto-correlation function for my >>> system >>> which have 128 cation and 128 anion. >>> >>> I am saving the trajectory at each 2 ps and using this trajectory for >>> further analysis. >>> >>> Can I save the dipole moment and three vectors at each 3 fs? >>> >>> >>> >>> Thanks >>> >>> Nilesh >>> >>> >>> >>> >> > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Dipole moment
Hello, I am calculating the dipole moment auto-correlation function for my system which have 128 cation and 128 anion. I am saving the trajectory at each 2 ps and using this trajectory for further analysis. Can I save the dipole moment and three vectors at each 3 fs? Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_dipole
Hello, I am calculating the dipole moment auto-correlation function for my system which have 128 cation and 128 anion. Due to the PBC, the function of the total dipole moment in time is not continuous. Can I removed PBC for g_dipole? Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_velacc
Hello, I am calculating the velocity auto-correlation function for my system which have 128 cation and 128 anion. How the program calculate the total velocity auto-correlation function? Does it average the velocity over all atoms at each time step? Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] PBC
Hello, I have question about periodic boundary condition. Suppose if one atom is going out of the box (x axis distance is more than L/2) and it will come inside the box from other side (distance-L). Distance before the pbc should be same or it will be different from center. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] grompp error
Hello, I am doing solvation dynamics for my system. When I am running grompp command I get the error. grompp -f md.mdp -c solvent-bmi-pf6-128.pdb -p solvent-bmi-pf6-128.top -o md-rerun.tpr Fatal error: No such combination rule 0 I using Gromacs VERSION 4.0.5. What this error means? Thanks NIlesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] (no subject)
Hello, I am doing solvation dynamics for my system. I have system with diatomic (PA---NE)solute surrounded by water molecules. I am running simulation for two differcent cases. 1. PA charge=0 and NE charge=0 : No charge on solute 2. PA charge=+1 and NE charge=-1 : Charge on solute For second case I am using rerun option to calculate the energy with charge for same configuration. grompp -f md.mdp -c solvent-bmi-pf6-128.pdb -p solvent-bmi-pf6-128.top -o md-rerun.tpr /opt/mpich_intel/ch-p4/bin/mpirun -machinefile cp -np 2 /usr/local/gromacs/bin/mdrun_mpi -s md-rerun.tpr -o md-rerun.trr -c solvent-bmi-pf6-128.pdb -e md-rerun.edr -rerun md.trr -g md-rerun.log The total energy difference between change and neutal is large around ~350 kj/mole. It should be around 30 kJ /mole. Can you tell why I getting large high energy differmece. I using Gromacs VERSION 4.0.5. NIlesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_hbond
Hello, How can I add chlorin atom as a acceptor in g_hbond. I am using Gromacs VERSION 4.0.7 NIlesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Graphene - force field
Hello, I am trying to run simulation of graphene oxide. I have 16 carbon atoms of same type. I am using opls force field. could make the .itp file and pasted here [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_071 CG 6 12.01100 0.00 A 3.5e-01 2.92880e-01 opls_072 CO 6 12.01100 0.265 A 3.5e-01 3.59824e-01 opls_116 OH 8 15.99940 -0.683 A 3.12000e-01 7.11280e-01 opls_117 HO 1 1.00800 0.418 A 0.0 0.0 [ bondtypes ] ; ij func b0 kb COOH 10.14100 133888.0 OHHO 10.09600 231375.0 CGCG 10.14000 392459.2 ; TRP,TYR,PHE CGCO 10.14000 392459.2 ; TRP,TYR,PHE [ angletypes ] ; ijk func th0 cth CG CO OH 190.000292.880 CO OH HO 1 108.500230.120 CG CG CG 1 120.000527.184 ; TYR(OL) [ dihedraltypes ] ; ijkl func coefficients ; OPLS Fourier function (func=5) CJ CJ CJ CJ 3 30.33400 0.0 -30.33400 0.0 0.0 0.0 ; CG CO OH HO 3 0.0 0.0 6.27600 0.0 CG CG CO OH 3 7.15882 -2.09200 2.77399 0.0 My question how can I step for the parameters ffoplsaa.rtp file. I made the parameters as follow [ SMA ] [ atoms ] CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 CO opls_072 0.265 2 CG opls_071 0.00 1 CG opls_071 0.00 1 CO opls_072 0.265 2 CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 OH opls_116-0.683 3 HO opls_117 0.000 4 OH opls_116-0.683 3 HO opls_117 0.000 4 [ bonds ] CG CG CG CO CO OH OH HO I am geting trouble to create .top file using pdb2gmx. Can you tell how to set up force field parameter for graphene. I am usinng Gromacs VERSION 4.0.7. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] dihedral angle
Hello, I am trying to calculate the dihedral angle between four points. I considered two planes (ABC & BCD) and calculate the dot products of two normals (n1 and n2)to these plane. theta=cos-1(n1.n2) I compared theeta values of dihedral angle with ampac and some values are negative. I am geting all positive value. Any one knows how to calculate sign of dihedral angle. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] box dimension
I used -pbc nojump to remove pbc effect. trjconv 3.trr -s 3.tpr -pbc nojump -o 500-11.pdb Basically I want to find the conformer close to center of box. Nilesh On Mon, October 17, 2011 6:36 pm, Mark Abraham wrote: > On 18/10/2011 7:05 AM, Nilesh Dhumal wrote: > >> Hello, >> >> >> I have saved the coordinates of snapshot from trajectory in pdb file. >> >> >> The dimesnion of box in pdb file are >> 32.805 32.805 32.805 90.00 90.00 90.00 P 1 >> >> >> I am trying to find atoms close to center of box. >> >> >> there are atoms whose distance from center is more that ~17 A. My >> center coordinates are 0.0 0.0 0.0. >> >> How is it possible? >> > > Molecules diffuse across periodic boundaries during the simulation. > While computing interactions, mdrun corrects for periodicity on the fly, > but does not trouble itself to guess what manner of post-processing you > would like to do. There is a suggested trjconv workflow on the the GROMACS > website. I suggest you try it. > > Mark > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] box dimension
Hello, I have saved the coordinates of snapshot from trajectory in pdb file. The dimesnion of box in pdb file are 32.805 32.805 32.805 90.00 90.00 90.00 P 1 I am trying to find atoms close to center of box. there are atoms whose distance from center is more that ~17 A. My center coordinates are 0.0 0.0 0.0. How is it possible? I am using Gromacs 4.0.7 version. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] trjconv:solute at the center
Ya, I want to center solute w.r.t to the solvent. I have more question, if I want to save the coordinates of a snapshot with no pbc effect, can I use -pbc nojump in trjconv. nilesh On Mon, October 17, 2011 1:34 pm, Tsjerk Wassenaar wrote: > Hey :) > > > The reference plays no role in centering. But I guess that Nilesh expects > centering of the solute w.r.t. to the solvent, or is looking at the > wrong center (tric/rect). > > Cheers, > > > Tsjerk > > > On Oct 17, 2011 7:06 PM, "Justin A. Lemkul" wrote: > > > Nilesh Dhumal wrote: > > Thanks Justin, > > Still solute is not at > center. > > > Is your reference frame (i.e. the .tpr file) centered? If not, centering > likely won't work as desired. I assumed that it was centered, per > normal system building procedures. > > -Justin > > >> Nilesh > > > On Mon, October 17, 2011 11:27 am, Justin A. Lemkul wrote: >> > >> >>> Nilesh Dhumal wrote... >>> > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] trjconv:solute at the center
Thanks Justin, Still solute is not at center. Nilesh On Mon, October 17, 2011 11:27 am, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> In 2nd step I choose system instaed of solvent. >> >> >> I could not make the solute at the center. >> >> > > Don't use -b and -e when running trjconv. I have found that PBC routines > are not always correctly applied when parsing out sections of the > trajectory. This can affect your ability to center the molecule. > > -Justin > > >> Thanks >> NIlesh >> >> >> On Mon, October 17, 2011 11:05 am, Justin A. Lemkul wrote: >> >> >>> Nilesh Dhumal wrote: >>> >>> >>>> Justin, >>>> >>>> >>>> >>>> I have 26 solute atoms and 3302 solvent atoms in my sytems (total >>>> 3328 >>>> atoms). >>>> >>>> >>>> 1. trjconv -f 3.trr -s 3.tpr -pbc mol -b 400 -e 600 -dt 1 -n >>>> 500-1.ndx >>>> -o >>>> 4-600.xtc >>>> here I choose group 0:system (3328 atoms) >>>> >>>> 2. trjconv -f 4-600.xtc -s 3.tpr -n 500-1.ndx -center -o >>>> 4-600-1.xtc >>>> >>>> >>>> >>>> For Centering I choose group: solute (26 atoms) >>>> For output I choose group : Solvent (3302 atoms) >>>> >>>> >>>> >>>> >>>> 3. trjconv -f 4-600-1.xtc -s 3.tpr -dump 500 -o 500-11.pdb >>>> >>>> >>>> >>>> Here I choose the group: 0 (system). >>>> >>>> >>>> >>>> I am geting for error for last command. >>>> >>>> >>>> >>>> Fatal error: >>>> Index[3302] 3303 is larger than the number of atoms in the >>>> trajectory file (3302). >>>> >>>> >>>> It look that there are no solute atoms in trajectory file. >>>> >>>> >>>> >>> In step 2, you chose to save only the solvent. >>> >>> >>> >>> -Justin >>> >>> >>> >>> -- >>> >>> >>> >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> >>> >>> >>> -- >>> gmx-users mailing listgmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >>> >>> >>> >>> >> >> >> > > -- > > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] trjconv:solute at the center
In 2nd step I choose system instaed of solvent. I could not make the solute at the center. Thanks NIlesh On Mon, October 17, 2011 11:05 am, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Justin, >> >> >> I have 26 solute atoms and 3302 solvent atoms in my sytems (total 3328 >> atoms). >> >> >> 1. trjconv -f 3.trr -s 3.tpr -pbc mol -b 400 -e 600 -dt 1 -n 500-1.ndx >> -o >> 4-600.xtc >> here I choose group 0:system (3328 atoms) >> >> 2. trjconv -f 4-600.xtc -s 3.tpr -n 500-1.ndx -center -o 4-600-1.xtc >> >> >> For Centering I choose group: solute (26 atoms) >> For output I choose group : Solvent (3302 atoms) >> >> >> >> 3. trjconv -f 4-600-1.xtc -s 3.tpr -dump 500 -o 500-11.pdb >> >> >> Here I choose the group: 0 (system). >> >> >> I am geting for error for last command. >> >> >> Fatal error: >> Index[3302] 3303 is larger than the number of atoms in the trajectory >> file (3302). >> >> >> It look that there are no solute atoms in trajectory file. >> >> > > In step 2, you chose to save only the solvent. > > > -Justin > > > -- > > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] trjconv:solute at the center
Justin, I have 26 solute atoms and 3302 solvent atoms in my sytems (total 3328 atoms). 1. trjconv -f 3.trr -s 3.tpr -pbc mol -b 400 -e 600 -dt 1 -n 500-1.ndx -o 4-600.xtc here I choose group 0:system (3328 atoms) 2. trjconv -f 4-600.xtc -s 3.tpr -n 500-1.ndx -center -o 4-600-1.xtc For Centering I choose group: solute (26 atoms) For output I choose group : Solvent (3302 atoms) 3. trjconv -f 4-600-1.xtc -s 3.tpr -dump 500 -o 500-11.pdb Here I choose the group: 0 (system). I am geting for error for last command. Fatal error: Index[3302] 3303 is larger than the number of atoms in the trajectory file (3302). It look that there are no solute atoms in trajectory file. Nilesh On Mon, October 17, 2011 7:25 am, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Hello, >> >> >> I have system with solute is surrounded by 256 solvent molecules. I run >> the simulation for 20 ns. I save the snap shot at 500 ps using >> following command. >> >> trjconv -f 3.trr -s 3.tpr -n 500-1.ndx -b 500.0 -e 501.0 -dt 1.0 -pbc >> nojump -center -o 500-11.pdb >> >> I tried to keep the solute at the center box. In visualization, the >> solute is not at center , its close to box edges. >> >> How can I keep the solute at the center. >> >> >> > > You're doing too many things at once. Split the trjconv operation: > > > 1. Run trjconv -pbc mol on the whole trajectory > 2. Run trjconv -center on the output of (1) > 3. Run trjconv -dump 500 on the output of (2) > > > -Justin > > >> I am using Gromacs 4.0.7 version. >> >> >> Thanks >> >> >> Nilesh >> >> >> >> >> >> >> >> >> >> >> > > -- > > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] trjconv:solute at the center
Hello, I have system with solute is surrounded by 256 solvent molecules. I run the simulation for 20 ns. I save the snap shot at 500 ps using following command. trjconv -f 3.trr -s 3.tpr -n 500-1.ndx -b 500.0 -e 501.0 -dt 1.0 -pbc nojump -center -o 500-11.pdb I tried to keep the solute at the center box. In visualization, the solute is not at center , its close to box edges. How can I keep the solute at the center. I am using Gromacs 4.0.7 version. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] snap shot
Hello, How can I save the coordinates (in pdb or xyz format) for a particular snap shot. Nilesh On Sat, October 8, 2011 10:06 am, lina wrote: > On Sat, Oct 8, 2011 at 2:21 AM, Nilesh Dhumal > wrote: > > >> Hello, >> >> >> I have a system with 128 emi (cations) and 128 Cl (anions). I run the >> simulation for 20 ns. >> >> I want to save snap-shot at 5ns, 10ns, 15ns and 20ns. >> >> > trjconv use -dt 5000 > >> >> I don't want to save snap shot for 128 ion-pairs. How can I take >> average over 128 ion pairs and save snap shot for a single ion pair. >> > I don't understand the average mean here? > if you wanna get the average.pdb in some time interval try g_rmsf -ox -b > -e > > > you may wait for some other better answers. > > >> Basically I want to use classical md geometry for quatum chemical >> calculation. >> >> I am using Gromacs 4.0.7 version. >> >> >> Thanks >> >> >> Nilesh >> >> >> >> >> >> >> >> >> >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >> >> > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] snap shot
Hello, I have a system with 128 emi (cations) and 128 Cl (anions). I run the simulation for 20 ns. I want to save snap-shot at 5ns, 10ns, 15ns and 20ns. I don't want to save snap shot for 128 ion-pairs. How can I take average over 128 ion pairs and save snap shot for a single ion pair. Basically I want to use classical md geometry for quatum chemical calculation. I am using Gromacs 4.0.7 version. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_rdf
Hello, I run a 5ns simulation for a single glucose molecule in gas phase. I tried to plot radial distribution function for O---H intramolecular interactions using following command. g_rdf -f 6.trr -s 6.tpr -n index -o In rdf.xvg file there is no data. Can you tell what could be the reason. I am using Gromacs 4.0.7 version. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] constraints on angle
Hello, How can I put constraints on an angle. I added following lines in .top file [ constraints ] 2 8 18 3 109.5 But its giving error. How can I put constraints on an angle. I am using Gromacs 4.0.7 version. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Velocity of atom
Hello, How can I print/calculate on velocity of a atom. I am using Gromacs 4.0.7 version. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Velocity autocorrelation function
Hello, Using g_velacc I can calculate the velocity autocorrelation function of a group as a vector. Can I calculate the velocity autocorrelation function as a scalar? I am using Gromacs 4.0.7 version. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] (no subject)
Hello, Using g_velacc I can calculate the velocity autocorrelation function of a group. Can I calculate the speed of a group instead of velocity ? I am using Gromacs 4.0.7 version. Thanks Nilesh vac.pdf Description: Adobe PDF document -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] (no subject)
Hello, I want to simulate system with 128 ionic liquids (128 cation+128 anion). I have made a pdb file with a single ionic liquids ion pairs. How can I genrate 128 ion pairs using single ion pair .pdb file. I am using Gromacs 4.0.7 version. Thanks Nilesh vac.pdf Description: Adobe PDF document -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_velacc
Hello, I am calculating the velocity autocorrelation function for my system. I have to calculate the g_velacc for 5 different groups within system. I have made the index file. I have also written .sh script g_velacc -f 6.trr -s 6.tpr -n glu-emi-dmp-128-no.ndx -nonormalize -o h20-vac.xvg 24 g_velacc -f 6.trr -s 6.tpr -n glu-emi-dmp-128-no.ndx -nonormalize -o h21-vac.xvg 25 g_velacc -f 6.trr -s 6.tpr -n glu-emi-dmp-128-no.ndx -nonormalize -o h24-vac.xvg 26 How can I select the group. In the above script 24, 25, 26 are the group numbers in index file. I am using Gromacs 4.0.7 version. Thanks Nilesh vac.pdf Description: Adobe PDF document -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_velacc
Hello, I am trying to calculate the velocity autocorrelation function for my system. I have a system with glucose + ionic liquids (128 emi (cations) and 128 Cl (anions)). I am not getting proper velocity autocorrelation function. g_velacc -f 6.trr -s 6.tpr -n glu-emi-cl-128-no.ndx -nonormalize -e 10 -o Attached the velocity autocorrelation function. I am using Gromacs 4.0.7 version. Thanks Nilesh vac.pdf Description: Adobe PDF document -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_velacc
Hello, I am trying to calcualte the velocity autocorrelation function for my system. I have a system with glucose + ionic liquids (128 emi (cations) and 128 Cl (anions)). I am not geting proper velocity autocorrelation function. g_velacc -f 6.trr -s 6.tpr -n glu-emi-cl-128-no.ndx -nonormalize -e 10 -o Attached the velocity autocorrelation function. I am using Gromacs 4.0.7 version. Thanks Nilesh vac.pdf Description: Adobe PDF document -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_velacc
Hello, I am trying to calcualte the velocity autocorrelation function for my system. I have a system with glucose + ionic liquids (128 emi (cations) and 128 Cl (anions)). I am not geting proper velocity autocorrelation function. g_velacc -f 6.trr -s 6.tpr -n glu-emi-cl-128-no.ndx -nonormalize -e 10 -o Attached the velocity autocorrelation function. I am using Gromacs 4.0.7 version. Thanks Nilesh vac.pdf Description: Adobe PDF document -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_dist
Hello, I have a system with 128 emi (cations) and 128 Cl (anions). I want to calculate how many CL atoms are in cutoff distance relative to hydorgen aotm of cation. I considered all CL atoms are distinguishable. Basically I want to calcualte the distance between each CL atom and correponing hydorgen and registered those CL atoms which are whthin cutoff. How can I do ? I am using Gromacs 4.0.7 version. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] rdf
Hello, I have a system with 128 emi (cations) and 128 Cl (anions). I want to study is there any bifurcated interaction between hydrogen of cation and CL atoms or CL atom interacting with 2 different hydrogen of cation. For this I considered all CL atoms are distinguishable. I am thinking to run rdf between each hydrogen and each cl atom (RDF 128 times). In my index file I made 3 groups for 3 different hydrogen and 128 groups for 128 cl atoms. I have to run 128 * 3 = 384 times rdf Is this the correct way? Is there any other easier way to do this? I am using Gromacs 4.0.7 version. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] rdf
Hello, I have a system with 128 emi (cations) and 128 Cl (anions). I want to study is there any bifurcated interaction between hydrogen of cation and CL atoms or CL atom interacting with 2 different hydrogen of cation. For this I considered all CL atoms are distinguishable. I am thinking to run rdf between each hydrogen and each cl atom (RDF 128 times). In my index file I made 3 groups for 3 different hydrogen and 128 groups for 128 cl atoms. I have to run 128 * 3 = 384 times rdf Is this the correct way? Is there any other easier way to do this? I am using Gromacs 4.0.7 version. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Lennard Jones interactions
Basically I want to calculate LJ interaction for OH bond. If I use eq. 4.5 in manual to calculate LJ interaction then zero. How can I calculate LJ interaction of a bond? Nilesh On Fri, June 10, 2011 3:00 pm, Andrew Paluch wrote: > The LJ interaction is 0. But you're asking about a bond. 1-2 > interactions are typically modeled with a harmonic potential. This is most > definitely not zero. > > > On Jun 10, 2011, at 2:54 PM, Nilesh Dhumal wrote: > > >> If eplilon of hydrogen atom is zero then the lennard jones >> interaction of OH bond (at 0.22nm)is also zero. >> Is it correct? >> >> >> I used equation 4.5 to calculate LJ energy. >> >> >> Nilesh >> >> >> On Fri, June 10, 2011 2:47 pm, Justin A. Lemkul wrote: >> >>> >> >>> >>> Nilesh Dhumal wrote: >>> >>> >>>> Hello, >>>> >>>> >>>> >>>> How can I calculate Lennard Jones interaction for two selected >>>> atoms with a specific distance? >>>> >>> >>> Using energygrps might be an option if you need to monitor the >>> interaction over time. Otherwise, if the distance is fixed, just plug >>> all the parameters into the LJ equation. In theory, you could >>> calculate the interactions this way over time, as well, even if the >>> distance changes. >>> >>> -Justin >>> >>> >>> >>>> I am using Gromacs 4.0.7 version. >>>> >>>> >>>> >>>> Thanks >>>> >>>> >>>> >>>> Nilesh >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>> >>> -- >>> >>> >>> >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> >>> >>> >>> -- >>> gmx-users mailing listgmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >>> >>> >>> >>> >> >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/Support/ >> Mailing_Lists/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/Support/Mailing_Lists >> > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Lennard Jones interactions
If eplilon of hydrogen atom is zero then the lennard jones interaction of OH bond (at 0.22nm)is also zero. Is it correct? I used equation 4.5 to calculate LJ energy. Nilesh On Fri, June 10, 2011 2:47 pm, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Hello, >> >> >> How can I calculate Lennard Jones interaction for two selected atoms >> with a specific distance? >> > > Using energygrps might be an option if you need to monitor the > interaction over time. Otherwise, if the distance is fixed, just plug all > the parameters into the LJ equation. In theory, you could calculate the > interactions this way over time, as well, even if the distance changes. > > -Justin > > >> I am using Gromacs 4.0.7 version. >> >> >> Thanks >> >> >> Nilesh >> >> >> >> >> >> >> > > -- > > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Lennard Jones interactions
Hello, How can I calculate Lennard Jones interaction for two selected atoms with a specific distance? I am using Gromacs 4.0.7 version. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] (no subject)
Hello, I want to calculate velocity autocorrelation function using 50 ps production trajectory. I have trajectory of 20 ns. I want to take 50 ps average over 20 ns trajectory to improve my result. How can do this average. I am using Gromacs 4.0.7 version. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_dipoles + tpbconv
Hello, I have a system with a glucose molecule. I want to calculate the dipole moment of a particular OH in glucose molecule.I made an index file which have a group containing atoms. [ O8 ] 8 18 10 is oxygen no. and 20 is hydroen no. But, if I try to use g_dipoles to get the dipole moment contribution from using following command: g_dipoles -f 6.trr -s 6.tpr -n index.ndx -corr mol -nonormalize -c I get the following error. Fatal error: index[1]=8 does not correspond to the first atom of a molecule I read on gmx-users mailing list. http://www.mail-archive.com/gmx-users@gromacs.org/msg40091.html Calculating a dipole moment of a possibly-charged species requires that there be a reference point, which is conventionally the center of mass of the molecule. This means all the atoms of the molecule have to be known, and g_dipoles assumes the index group consists of whole molecules. So to do the partition you want, you will need to provide the same molecules, but with zero charges. That will mean making a copy of your .top and hacking those charges to zero to generate a new such .tpr. Actually, tpbconv has the ability to set the charges of a group in a .tpr to zero. So I tried tpbconv -f 6.trr -s 6.tpr -n glu-emi-cl-128-no.ndx -e 6.edr -o zero.tpr I got the error segmentataion fault How can I solve this problem to calcualte the dipole moment of a bond? I am using gromacs version 4.0.7. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_velacc
How can I calculate the velocity autocorrelation function of a bond with Gromacs? Nilesh On Fri, May 27, 2011 8:31 am, David van der Spoel wrote: > On 2011-05-27 14.26, Nilesh Dhumal wrote: > >> I am calculating OH stretching frequency by fourier transform of >> velocity autocorrelation function. >> >> I could calculate the OH stretching frequnecy by calculating fourier >> transform of OH bond. >> >> I want to know how gromacs calculate the velocity autocorrelation >> function of a bond (If I define a bond in index file). >> >> Does is subtract the velocity of hydrogen from oxygen and then >> calculate the autocorrelation function? >> > No, see below! There is no tool that does exactly what you want, however > doing the velacc of just the hydrogen will come close. >> Nilesh >> >> >> >> >> >> On Fri, May 27, 2011 2:37 am, David van der Spoel wrote: >> >>> On 2011-05-26 22.48, Nilesh Dhumal wrote: >>> >>> >>>> Hello, >>>> >>>> >>>> >>>> I have calculated the velocity autocorrelation function of OH bond >>>> in glucose molecule. For this calculation I modified the index file. >>>> The >>>> modified part is pasted below. >>>> >>>> [ O10 ] >>>> 10 20 >>>> >>>> >>> >>> where is the hydrogen? g_velacc knows nothing about bonds just atoms. >>> >>> >>>> >>>> 10 is oxygen no. and 20 is oxygen. >>>> >>>> >>>> >>>> I used following command to calculate the velocity autocorrelation >>>> function. >>>> >>>> g_velacc -f 6.trr -s 6.tpr -n index.ndx -e 100 -nonormalize -o >>>> >>>> >>>> My question is how does the prog. calculate the velocity >>>> autocorrlation function. >>>> >>>> Does is subtract the velocity of hydrogen from oxygen and then >>>> calculate the autocorrelation function? >>>> >>>> I am using gromacs version 4.0.7. >>>> >>>> >>>> >>>> Thanks >>>> >>>> >>>> >>>> Nilesh >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>> >>> >>> -- >>> David van der Spoel, Ph.D., Professor of Biology >>> Dept. of Cell& Molec. Biol., Uppsala University. >>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. >>> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing >>> listgmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >>> >>> >>> >>> >> >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: g_velacc
How can I calculate the velocity autocorrelation function of a bond with Gromacs? Nilesh On Fri, May 27, 2011 8:32 am, Vitaly Chaban wrote: > As I said before, g_velacc treats all the atoms in your index file as > if they were identical. It does NOT subtract anything. > > > > > On Fri, May 27, 2011 at 8:19 AM, Nilesh Dhumal > wrote: > >> I am calculating OH stretching frequency by fourier transform of >> velocity autocorrelation function. >> >> I could calculate the OH stretching frequnecy by calculating fourier >> transform of OH bond. >> >> I want to know how gromacs calculate the velocity autocorrelation >> function of a bond (If I define a bond in index file). >> >> Does is subtract the velocity of hydrogen from oxygen and then >> calculate the autocorrelation function? >> >> Nilesh >> >> >> >> On Fri, May 27, 2011 8:11 am, Vitaly Chaban wrote: >> >>> It does not change the situation, I believe. >>> >>> >>> >>> What is the sense of calculating such ACF? In order to understand the >>> cross-correlation between the bonded atoms? It will be huge as I >>> understand. >>> >>> >>> -- >>> Dr. Vitaly V. Chaban, Department of Chemistry >>> University of Rochester, Rochester, New York 14627-0216 >>> >>> >>> >>> >>> >>> >>> On Fri, May 27, 2011 at 8:07 AM, Nilesh Dhumal >>> >>> wrote: >>> >>> >>>> 20 is hydrogen atom. >>>> Sorry its typing mistake. >>>> >>>> >>>> >>>> Nilesh >>>> >>>> >>>> >>>> On Fri, May 27, 2011 3:52 am, Vitaly Chaban wrote: >>>> >>>> >>>>>> >>>> >>>>>> Hello, >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> I have calculated the velocity autocorrelation function of OH >>>>>> bond in glucose molecule. For this calculation I modified the >>>>>> index file. The >>>>>> modified part is pasted below. >>>>>> >>>>>> >>>>>> >>>>>> [ O10 ] >>>>>> 10 20 >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> 10 is oxygen no. and 20 is oxygen. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> I used following command to calculate the velocity >>>>>> autocorrelation function. >>>>>> >>>>>> g_velacc -f 6.trr -s 6.tpr -n index.ndx -e 100 -nonormalize >>>>>> -o >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> My question is how does the prog. calculate the velocity >>>>>> autocorrlation function. >>>>>> >>>>>> >>>>>> Does is subtract the velocity of hydrogen from oxygen and then >>>>>> calculate the autocorrelation function? >>>>> >>>>> >>>>> >>>>> The program acts as if your hydrogen and oxygen are identical >>>>> atoms. >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Dr. Vitaly V. Chaban, Department of Chemistry >>>>> University of Rochester, Rochester, New York 14627-0216 >>>>> -- >>>>> gmx-users mailing list gmx-users@gromacs.org >>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>>> Please search the archive at >>>>> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lis >>>>> >>>>> >>> >>> >> >> >> > > > > -- > Dr. Vitaly V. Chaban, Department of Chemistry > University of Rochester, Rochester, New York 14627-0216 > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_velacc
I am calculating OH stretching frequency by fourier transform of velocity autocorrelation function. I could calculate the OH stretching frequnecy by calculating fourier transform of OH bond. I want to know how gromacs calculate the velocity autocorrelation function of a bond (If I define a bond in index file). Does is subtract the velocity of hydrogen from oxygen and then calculate the autocorrelation function? Nilesh On Fri, May 27, 2011 2:37 am, David van der Spoel wrote: > On 2011-05-26 22.48, Nilesh Dhumal wrote: > >> Hello, >> >> >> I have calculated the velocity autocorrelation function of OH bond >> in glucose molecule. For this calculation I modified the index file. The >> modified part is pasted below. >> >> [ O10 ] >> 10 20 >> > > where is the hydrogen? g_velacc knows nothing about bonds just atoms. > >> >> 10 is oxygen no. and 20 is oxygen. >> >> >> I used following command to calculate the velocity autocorrelation >> function. >> >> g_velacc -f 6.trr -s 6.tpr -n index.ndx -e 100 -nonormalize -o >> >> >> My question is how does the prog. calculate the velocity autocorrlation >> function. >> >> Does is subtract the velocity of hydrogen from oxygen and then >> calculate the autocorrelation function? >> >> I am using gromacs version 4.0.7. >> >> >> Thanks >> >> >> Nilesh >> >> >> >> >> >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: g_velacc
20 is hydrogen atom. Sorry its typing mistake. Nilesh On Fri, May 27, 2011 3:52 am, Vitaly Chaban wrote: >> >> Hello, >> >> >> I have calculated the velocity autocorrelation function of OH bond >> in glucose molecule. For this calculation I modified the index file. The >> modified part is pasted below. >> >> [ O10 ] >> 10 20 >> >> >> 10 is oxygen no. and 20 is oxygen. >> >> >> I used following command to calculate the velocity autocorrelation >> function. >> >> g_velacc -f 6.trr -s 6.tpr -n index.ndx -e 100 -nonormalize -o >> >> >> >> My question is how does the prog. calculate the velocity autocorrlation >> function. >> >> Does is subtract the velocity of hydrogen from oxygen and then >> calculate the autocorrelation function? > > > > The program acts as if your hydrogen and oxygen are identical atoms. > > > > -- > Dr. Vitaly V. Chaban, Department of Chemistry > University of Rochester, Rochester, New York 14627-0216 > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_velacc
Hello, I have calculated the velocity autocorrelation function of OH bond in glucose molecule. For this calculation I modified the index file. The modified part is pasted below. [ O10 ] 10 20 10 is oxygen no. and 20 is oxygen. I used following command to calculate the velocity autocorrelation function. g_velacc -f 6.trr -s 6.tpr -n index.ndx -e 100 -nonormalize -o My question is how does the prog. calculate the velocity autocorrlation function. Does is subtract the velocity of hydrogen from oxygen and then calculate the autocorrelation function? I am using gromacs version 4.0.7. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_velacc
Hello, I am trying to calculate the velocity autocorrelation function of OH bond in glucose molecule. The calculate velocity autocorrelation function is not smooth. Its fluctuating a lot so I am geting wide/think line. Why I am not geting a smooth line? I am using gromacs version 4.0.7. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] dipole moment
Basically I want to calculate the stretching vibration of the bond by fourier transfrom of dipole momenet autocorrelation fucntion or velocity autocorrelation function. Before going for vibration I wanted to check the fluctuation of dipole moment along the simulation. Can I calculate the velocity autocorrelation function for a bond. Nilesh On Wed, May 25, 2011 12:37 pm, David van der Spoel wrote: > On 2011-05-25 18.03, Nilesh Dhumal wrote: > >> Thanks for reply. >> >> >> Here are more details about my simulation. >> >> >> I have glucose molecule in my system. I am interested in change in >> dipole moment of OH bond of glucose along the simulation. > > The OH group is not neutral so your dipole is meaningless (position > dependent). > > Otherwise the charges are constant and the fluctuation in bond length > (if you have a flexible molecule) will be small, or zero with > constraints. You should think what you want to get out. What experiment you > want to compare to. >> >> I have made the index file. >> >> >> How can I select two groups (oxygen and hydrogen) or should I put >> particular oxygen and hydrogen in same group (manually). >> >> Nilesh >> >> >> On Wed, May 25, 2011 11:59 am, David van der Spoel wrote: >> >>> On 2011-05-25 17.36, Nilesh Dhumal wrote: >>> >>> >>>> I want to see the change in dipole moment alond the simulation. >>>> >>>> >>> g_dipoles -h >>> >>>> >>>> >>>> NIlesh >>>> >>>> >>>> >>>> On Wed, May 25, 2011 11:32 am, David van der Spoel wrote: >>>> >>>> >>>>> On 2011-05-25 17.14, Nilesh Dhumal wrote: >>>>> >>>>> >>>>> >>>>>> Hello, >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> Can I calculate a dipole moment of a particular bond? >>>>>> >>>>>> >>>>>> >>>>> It is easier to do it manually. Otherwise g_dipoles with a >>>>> suitable index file would do it. The sum of charges has to be zero >>>>> of course. >>>>>> >>>>>> I am using gromacs version 4.0.7. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> Thanks >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> Nilesh >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> -- >>>>> David van der Spoel, Ph.D., Professor of Biology >>>>> Dept. of Cell& Molec. Biol., Uppsala University. >>>>> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. >>>>> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users >>>>> mailing listgmx-users@gromacs.org >>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>>> Please search the archive at >>>>> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>> >>> >>> -- >>> David van der Spoel, Ph.D., Professor of Biology >>> Dept. of Cell& Molec. Biol., Uppsala University. >>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. >>> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing >>> listgmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >>> >>> >>> >>> >> >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] dipole moment
Thanks for reply. Here are more details about my simulation. I have glucose molecule in my system. I am interested in change in dipole moment of OH bond of glucose along the simulation. I have made the index file. How can I select two groups (oxygen and hydrogen) or should I put particular oxygen and hydrogen in same group (manually). Nilesh On Wed, May 25, 2011 11:59 am, David van der Spoel wrote: > On 2011-05-25 17.36, Nilesh Dhumal wrote: > >> I want to see the change in dipole moment alond the simulation. >> > g_dipoles -h > >> >> >> NIlesh >> >> >> On Wed, May 25, 2011 11:32 am, David van der Spoel wrote: >> >>> On 2011-05-25 17.14, Nilesh Dhumal wrote: >>> >>> >>>> Hello, >>>> >>>> >>>> >>>> Can I calculate a dipole moment of a particular bond? >>>> >>>> >>> It is easier to do it manually. Otherwise g_dipoles with a suitable >>> index file would do it. The sum of charges has to be zero of course. >>>> >>>> I am using gromacs version 4.0.7. >>>> >>>> >>>> >>>> Thanks >>>> >>>> >>>> >>>> Nilesh >>>> >>>> >>>> >>>> >>>> >>> >>> >>> -- >>> David van der Spoel, Ph.D., Professor of Biology >>> Dept. of Cell& Molec. Biol., Uppsala University. >>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. >>> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing >>> listgmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >>> >>> >>> >>> >> >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] dipole moment
I want to see the change in dipole moment alond the simulation. NIlesh On Wed, May 25, 2011 11:32 am, David van der Spoel wrote: > On 2011-05-25 17.14, Nilesh Dhumal wrote: > >> Hello, >> >> >> Can I calculate a dipole moment of a particular bond? >> > It is easier to do it manually. Otherwise g_dipoles with a suitable > index file would do it. The sum of charges has to be zero of course. >> >> I am using gromacs version 4.0.7. >> >> >> Thanks >> >> >> Nilesh >> >> >> >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] dipole moment
Hello, Can I calculate a dipole moment of a particular bond? I am using gromacs version 4.0.7. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_sdf
Hello, I have a system with glucose + ionic liquids (cation + anion). I am trying calculate distribution of cation and anion around glucose molecule using g_sdf. I want to plot distribution of cation and anion is same figure. I run the following command g_sdf -f 3.trr -s 3.tpr -n glu-emi-dmp-128-no.ndx -mode 2 -o -r I selected two atoms from glucose and 3rd and 4th groups are cation and anion respectively. All the coordinates in refmol.gro are zero. I am using gromacs version 4.0.7. Why all the coordinates in refmol.gro are zero. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: water dimer is gas phase
I run the same mdp files for glucose in vaccum. I ma geting the proper results, I can visualize the strucutre properly in VMD. If I use same for water why I am not geting proper structure ? Nilesh On Fri, May 20, 2011 9:48 am, Erik Marklund wrote: > Exactly. So now is the time for skillful scripting. > > > Erik > > > Nilesh Dhumal skrev 2011-05-20 15.31: > >> I used the same topology file to run 256 water molecules simulation and >> I >> got the proper result (compared with reported one). >> >> The problem is to visualize the trajectory in VMD since gromacs fails >> to write valid pdb files when the coordinates are too large. >> >> Nilesh >> >> >> >> On Fri, May 20, 2011 5:22 am, Erik Marklund wrote: >> >>> Justin A. Lemkul skrev 2011-05-19 22.42: >>> >>> >>>> >>>> Vitaly Chaban wrote: >>>> >>>> >>>>>> For vacuum systems, "pbc = no" in conjunction with zero cutoffs >>>>>> is correct to obtain a gas-phase system. >>>>> >>>>> For reasonably large box, this is the same heck. >>>>> >>>>> >>>>> >>>> Setting a box size and using "pbc = xyz" precludes the use of >>>> infinite cutoffs, which should be the most rigorously correct way to >>>> treat this type of system. With PBC, there are long-range effects >>>> that should be avoided. >>>> >>>>> Nilesh: visualize your system, using VMD or ngmx. The behavior of >>>>> your molecular cluster during the first ps will provide an >>>>> answer. Are you sure that your topology is healthy? >>>>> >>>> I agree with this. The system should be going absolutely haywire >>>> :) >>>> >>>> >>>> >>>> -Justin >>>> >>>> >>>> >>> Yes, this is a good test, and the topology should be inspected. >>> However, >>> the observed result is expected for this system. A water dimer coupled >>> to a thermostat will dissociate eventually (pretty rapidly) at 300 K. >>> The water >>> molecules themselves seem intact. The problem with visualization comes >>> from the fact that gromacs fails to write valid pdb files when the >>> coordinates are too large. I called this a bug on the developer list >>> one or two years ago since this generates pdb files that gromacs >>> itself can't read, but the other developers didn't catch on. You can >>> postprocess the pdb and cap the coordinates so that they're confined >>> to the range that the pdb format allows, but note that this will mess >>> up the water moleucles as they get very far apart. >>> >>> Erik >>> >>> >>> >>> -- >>> --- >>> Erik Marklund, PhD student >>> Dept. of Cell and Molecular Biology, Uppsala University. >>> Husargatan 3, Box 596,75124 Uppsala, Sweden >>> phone:+46 18 471 4537fax: +46 18 511 755 >>> er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ >>> >>> -- >>> gmx-users mailing listgmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >>> >>> >>> >>> >> > > > -- > --- > Erik Marklund, PhD student > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596,75124 Uppsala, Sweden > phone:+46 18 471 4537fax: +46 18 511 755 > er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: water dimer is gas phase
I used the same topology file to run 256 water molecules simulation and I got the proper result (compared with reported one). The problem is to visualize the trajectory in VMD since gromacs fails to write valid pdb files when the coordinates are too large. Nilesh On Fri, May 20, 2011 5:22 am, Erik Marklund wrote: > Justin A. Lemkul skrev 2011-05-19 22.42: > >> >> >> Vitaly Chaban wrote: >> For vacuum systems, "pbc = no" in conjunction with zero cutoffs is correct to obtain a gas-phase system. >>> >>> >>> For reasonably large box, this is the same heck. >>> >>> >> >> Setting a box size and using "pbc = xyz" precludes the use of infinite >> cutoffs, which should be the most rigorously correct way to treat this >> type of system. With PBC, there are long-range effects that should be >> avoided. >> >>> Nilesh: visualize your system, using VMD or ngmx. The behavior of >>> your molecular cluster during the first ps will provide an answer. Are >>> you sure that your topology is healthy? >>> >> >> I agree with this. The system should be going absolutely haywire :) >> >> >> -Justin >> >> > Yes, this is a good test, and the topology should be inspected. However, > the observed result is expected for this system. A water dimer coupled to a > thermostat will dissociate eventually (pretty rapidly) at 300 K. The water > molecules themselves seem intact. The problem with visualization comes > from the fact that gromacs fails to write valid pdb files when the > coordinates are too large. I called this a bug on the developer list one > or two years ago since this generates pdb files that gromacs itself can't > read, but the other developers didn't catch on. You can postprocess the > pdb and cap the coordinates so that they're confined to the range that the > pdb format allows, but note that this will mess up the water moleucles as > they get very far apart. > > Erik > > > -- > --- > Erik Marklund, PhD student > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596,75124 Uppsala, Sweden > phone:+46 18 471 4537fax: +46 18 511 755 > er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: water dimer is gas phase
if I set pbc=xyz in energy minimization mdp file then I get following error ERROR: can only have neighborlist cut-off zero (=infinite) with coulombtype = Cut-off or coulombtype = User and simple neighborsearch without periodic boundary conditions (pbc = no) and rcoulomb and rvdw set to zero ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist. Nilesh On Thu, May 19, 2011 3:57 pm, Vitaly Chaban wrote: >> the equlibration file I used >> >> title = cpeptid position restraining cpp >> = /usr/bin/cpp >> constraints = none integrator = md dt >> = 0.001 ; ps ! >> nsteps = 100 ; total 1.0 ps. nstcomm = >> 1 >> nstxout = 1 nstvout = 1 nstfout >> = 0 >> nstlog = 10 nstenergy = 10 nstlist = >> 10 >> ns_type = simple comm_mode = none coulombtype >> = cut-off >> vdwtype = cut-off rlist = 0.0 rcoulomb >> = 0.0 >> rvdw = 0.0 pbc = no fourierspacing = >> 0.12 >> fourier_nx = 0 fourier_ny = 0 fourier_nz >> = 0 >> pme_order = 4 ewald_rtol = 1e-5 optimize_fft = >> yes ; Berendsen temperature coupling is on >> Tcoupl = nose-hoover >> tau_t = 0.1 tc-grps =system ref_t = 298 ; Pressure coupling is on >> Pcoupl = NO ;Parrinello-Rahman >> pcoupltype = isotropic tau_p = 2.0 compressibility >> = 4.5e-5 >> ref_p = 1.0 ; Generate velocites is on at 300 K. >> gen_vel = yes gen_temp = 298.0 gen_seed >> = 173529 >> >> >> Is ther any thing wrong with my mdp files. >> WHy they is so much change is cooridnates in the .pdb file. >> >> > > > > Nilesh: > > > Set periodic conditions. This will restrict the coordinates to small > numbers. > > > -- > Dr. Vitaly V. Chaban, Department of Chemistry > University of Rochester, Rochester, New York 14627-0216 > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] water dimer is gas phase
Hello, I am trying a simulation for water dimer in vaccum (gas phase). Here I run the simulation with following steps This is the .pdb file before energy minimization TITLE S C A M O R G REMARKTHIS IS A SIMULATION BOX CRYST13.0003.0003.000 90.00 90.00 90.00 P 1 1 MODEL1 ATOM 1 OW WAT 1 0.317 1.494 1.565 1.00 0.00 ATOM 2 HW1 WAT 1 -0.091 2.293 1.258 1.00 0.00 ATOM 3 HW2 WAT 1 -0.144 0.788 1.129 1.00 0.00 ATOM 4 OW WAT 2 3.172 1.515 1.356 1.00 0.00 ATOM 5 HW1 WAT 2 2.224 1.482 1.459 1.00 0.00 ATOM 6 HW2 WAT 2 3.522 1.427 2.231 1.00 0.00 TER ENDMDL I run the energy minimization grompp -f minim-gas.mdp -c dimer.pdb -p dimer.top -o dimer.tpr mdrun -pd -s dimer.tpr -o dimer.trr -c dimer.pdb -e dimer.edr -g dimer.log I got the following file which I could visualize TITLE Protein MODEL1 ATOM 1 OW WAT 1 0.351 1.490 1.592 1.00 0.00 ATOM 2 HW1 WAT 1 -0.106 2.335 1.248 1.00 0.00 ATOM 3 HW2 WAT 1 -0.162 0.750 1.112 1.00 0.00 ATOM 4 OW WAT 2 3.198 1.519 1.321 1.00 0.00 ATOM 5 HW1 WAT 2 2.174 1.481 1.457 1.00 0.00 ATOM 6 HW2 WAT 2 3.544 1.423 2.268 1.00 0.00 TER ENDMDL minim-gas.mdp file title = cpeptide cpp = /usr/bin/cpp constraints = none integrator = steep dt = 0.002; ps ! nsteps = 5 nstlist = 1 coulombtype = cut-off vdwtype = cut-off ns_type = simple rlist = 0.0 rcoulomb= 0.0 rvdw= 0.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes pbc = no ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 the I run equlibration grompp -f minim-pr.mdp -c dimer.pdb -p dimer.top -o dimer.tpr mdrun -pd -s dimer.tpr -o dimer.trr -c dimer.pdb -e dimer.edr -g dimer.log I got the following file which I could not visualize TITLE Protein MODEL1 ATOM 1 OW WAT 1-2737.208 974.242-2091.510 1.00 0.00 ATOM 2 HW1 WAT 1-2737.949 973.910-2090.885 1.00 0.00 ATOM 3 HW2 WAT 1-2736.363 974.004-2091.048 1.00 0.00 ATOM 4 OW WAT 22740.655-971.0932094.500 1.00 0.00 ATOM 5 HW1 WAT 22740.852-971.7332093.873 1.00 0.00 ATOM 6 HW2 WAT 22740.420-971.4722095.431 1.00 0.00 TER ENDMDL the equlibration file I used title = cpeptid position restraining cpp = /usr/bin/cpp constraints = none integrator = md dt = 0.001; ps ! nsteps = 100 ; total 1.0 ps. nstcomm = 1 nstxout = 1 nstvout = 1 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = simple comm_mode = none coulombtype = cut-off vdwtype = cut-off rlist = 0.0 rcoulomb= 0.0 rvdw= 0.0 pbc = no fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on Tcoupl = nose-hoover tau_t = 0.1 tc-grps =system ref_t = 298 ; Pressure coupling is on Pcoupl = NO ;Parrinello-Rahman pcoupltype = isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 298.0 gen_seed= 173529 Is ther any thing wrong with my mdp files. WHy they is so much change is cooridnates in the .pdb file. I am using gromacs version 4.0.7. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: [gmx-developers] flexible water model
Hello Justin, I used 0.1fs timestep and I could get dielectric constant around 56 which looks ok. To get the dielectric constant around ~75, should I reduce the timestep around 0.05fs. I used temperature 298k for my simulation and average tmep. I got is 297.83 K. I am doing NPT and used 1.0 bar as reference pressure in my .mdp. I am getting average pressure around 2.58 bar. I run the equilibration for 1ns. Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature 297.8310.968710.9643 -0.00165807 -1.07774 Pressure (bar) 2.575514246.514246.51 -0.0360116 -23.4075 Why there is change in pressure? Is there any wrong with simulation? Nilesh On Wed, May 11, 2011 4:18 pm, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> I have general question. If this parameters are not giving the proper >> results then How come I get the proper results with same parameter if I >> use 1/2 value of Kbond with the same parameters. >> > > Random chance, I imagine. Your .mdp settings are not correct and the > cutoffs are unreasonably short for any modern force field. If you're > seeking to reproduce others' work, then you have to use the same protocol. > You're not > doing that. > >> I checked the temp when I use half value of Kbond and it goes max. >> ~320. >> >> > > This would also indicate instability. You managed to get a "correct" > result for one observable from an incorrect simulation wherein the > thermodynamic observables do not correspond to what you have set. > > The way I found all of this out was first and foremost by watching the > trajectory. After about 30 ps, the water molecules freeze in place and > vibrate as if they are about to shear apart. At this exact time, the > value of epsilon (from epsilon.xvg, output by g_dipoles) plummets down, > after having steadily increased for the first 30 ps, as expected. The > temperature spikes and the pressure begins to oscillate by +/- 10^5, far > higher than what it should for a system of a few hundred water molecules. > > Watch your trajectories, make sure you're getting the right average > temperature and pressure, and that all your other energetic terms > stabilize, then analyze the result of the simulation. Otherwise, any > inferred output is meaningless. > > -Justin > > >> Nilesh >> >> >> On Wed, May 11, 2011 4:03 pm, Justin A. Lemkul wrote: >> >> >>> Nilesh Dhumal wrote: >>> >>> >>>> Hello Justin, >>>> >>>> >>>> >>>> I used 0.5 fs time step and still I got dielectric constant ~2. >>>> >>>> >>>> >>>> This is the md.mdp file I used. I checked the temperature it >>>> didn't go more than ~ 320 K. >>>> >>> Still, that's unacceptable if your ref_t is 295. The fact that the >>> temperature is still rocketing up suggests the same instability I >>> found. >>> >>>> title = cpeptide MD cpp = >>>> /usr/bin/cpp >>>> integrator = md dt = 0.001; ps ! >>>> nsteps = 650 ; total 5 ps. >>>> nstcomm = 1000 nstxout = 1000 nstvout = >>>> 1000 >>>> nstfout = 1 nstlist = 1 ns_type >>>> = >>>> grid rlist = 0.6 rcoulomb= 0.6 rvdw = >>>> 0.7 >>>> >>>> >>> These cutoffs make no sense. The paper you've cited used 0.9 nm. If >>> you're trying to reproduce previous work, use the same settings. >>> >>>> coulombtype = PME vdwtype = cut-off >>> Similarly here, you haven't applied dispersion correction, which you >>> should, per the methods used in the JCP article. >>> >>> -Justin >>> >>> >>> >>>> pbc = xyz fourierspacing = 0.12 fourier_nx = 0 >>>> fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = >>>> 1e-5 >>>> optimize_fft= yes ; Berendsen temperature coupling is on >>>> Tcoupl = v-rescale >>>> tau_t = 0.1 tc-grps =system ref_t = 295 ; Pressure coupling is >>>> on Pcoupl = parrinello-rahman >>>> pcoupltype = isotropic tau_p = 0.5 >>>> compressibility = 4.5e-5 >>>> ref_p
[gmx-users] pressure in NPT and NVT
Hello, I am using NPT simulation for water - spce model (opls-aa force field). I have the reference pressure set at ref_p = 1.0 bar. I checked the average pressure using g_energy and it is 2.81972 bar. Why there increase in pressure? For NVT simulatin I get the value around average pressure 710.685 bar. I am running the simulation at 295 k and average temp. is 294.98 K which look ok. Can you tell why there is increase in pressure for NPT and why there is so high value of pressure in NVT. I am using gromacs version 4.0.7. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: [gmx-developers] flexible water model
I have general question. If this parameters are not giving the proper results then How come I get the proper results with same parameter if I use 1/2 value of Kbond with the same parameters. I checked the temp when I use half value of Kbond and it goes max. ~320. Nilesh On Wed, May 11, 2011 4:03 pm, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Hello Justin, >> >> >> I used 0.5 fs time step and still I got dielectric constant ~2. >> >> >> This is the md.mdp file I used. I checked the temperature it didn't go >> more than ~ 320 K. >> > > Still, that's unacceptable if your ref_t is 295. The fact that the > temperature is still rocketing up suggests the same instability I found. > >> title = cpeptide MD cpp = /usr/bin/cpp >> integrator = md dt = 0.001; ps ! nsteps >> = 650 ; total 5 ps. >> nstcomm = 1000 nstxout = 1000 nstvout >> = 1000 >> nstfout = 1 nstlist = 1 ns_type = >> grid rlist = 0.6 rcoulomb= 0.6 rvdw >> = 0.7 >> > > These cutoffs make no sense. The paper you've cited used 0.9 nm. If > you're trying to reproduce previous work, use the same settings. > >> coulombtype = PME vdwtype = cut-off > > Similarly here, you haven't applied dispersion correction, which you > should, per the methods used in the JCP article. > > -Justin > > >> pbc = xyz fourierspacing = 0.12 fourier_nx = 0 >> fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol >> = 1e-5 >> optimize_fft= yes ; Berendsen temperature coupling is on >> Tcoupl = v-rescale >> tau_t = 0.1 tc-grps =system ref_t = 295 ; Pressure coupling is on >> Pcoupl = parrinello-rahman >> pcoupltype = isotropic tau_p = 0.5 compressibility >> = 4.5e-5 >> ref_p = 1.0 ; Generate velocites is on at 300 K. >> gen_vel = yes gen_temp= 295.0 gen_seed >> = 173529 >> >> >> >> Nilesh >> >> >> >> On Tue, May 10, 2011 6:14 pm, Justin A. Lemkul wrote: >> >> >>> The gmx-developers list is not the forum for these types of >>> questions. I am replying via gmx-users, which is where the discussion >>> should stay. >>> >>> I took a few minutes to dig into this. My conclusion is that your >>> system is not stable. I would encourage you to analyze the >>> temperature and pressure of your systems that are giving odd results. >>> When I used the >>> topology you provided, the temperature spiked to over 600 K and the >>> box began to oscillate extensively as if the system were about to >>> explode. The resulting epsilon value was about 1.6. >>> >>> >>> >>> If I reduce the timestep to 0.5 fs, the results are much more >>> reasonable, and using the Ka and Kb values in the paper (not halved!) >>> I get a much >>> more sensible result, even after just 100 ps. It looks to me as if >>> the combination of these parameters and a 1-fs timestep is not >>> entirely stable. I know the original authors used dt = 1 fs, but the >>> point remains. >>> >>> -Justin >>> >>> >>> >>> Nilesh Dhumal wrote: >>> >>> >>>> Hello, >>>> >>>> >>>> >>>> I am using flexible water model for my system. I am referring a >>>> paper J. >>>> Chem. Phys. 124, 024503 (2006). Author have used Amber type force >>>> field. >>>> >>>> >>>> i.e. 1/2 Kbond (r-req)**2 + 1/2 Kangle(theta-thetaeq)**2. >>>> >>>> Kbond = 443153.3808 kJ/mol nm**2 >>>> >>>> >>>> >>>> Kangle= 317.5656 kJ/mol rad**2. >>>> >>>> >>>> >>>> I am using olss-aa force field parameters in Gromacs VERSION >>>> 4.0.7. >>>> >>>> >>>> >>>> I checked some papers in which author have used oplsaa force field >>>> in Gromacs. 1/2 factor is not in opls force field if I compare opls >>>> and amber. >>>> >>>> >>>> I didnt get the proper dielectric constant for water when I used >>>> the parameters reported in paper >>>> >>>> (Kbond = 443153.3808 kJ/mol nm**2,K
Re: [gmx-users] Re: [gmx-developers] flexible water model
Hello Justin, I used 0.5 fs time step and still I got dielectric constant ~2. This is the md.mdp file I used. I checked the temperature it didn't go more than ~ 320 K. title = cpeptide MD cpp = /usr/bin/cpp integrator = md dt = 0.001; ps ! nsteps = 650 ; total 5 ps. nstcomm = 1000 nstxout = 1000 nstvout = 1000 nstfout = 1 nstlist = 1 ns_type = grid rlist = 0.6 rcoulomb= 0.6 rvdw= 0.7 coulombtype = PME vdwtype = cut-off pbc = xyz fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc-grps =system ref_t = 295 ; Pressure coupling is on Pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 295.0 gen_seed= 173529 Nilesh On Tue, May 10, 2011 6:14 pm, Justin A. Lemkul wrote: > > The gmx-developers list is not the forum for these types of questions. I > am replying via gmx-users, which is where the discussion should stay. > > I took a few minutes to dig into this. My conclusion is that your system > is not stable. I would encourage you to analyze the temperature and > pressure of your systems that are giving odd results. When I used the > topology you provided, the temperature spiked to over 600 K and the box > began to oscillate extensively as if the system were about to explode. > The resulting epsilon value was about 1.6. > > > If I reduce the timestep to 0.5 fs, the results are much more reasonable, > and using the Ka and Kb values in the paper (not halved!) I get a much > more sensible result, even after just 100 ps. It looks to me as if the > combination of these parameters and a 1-fs timestep is not entirely > stable. I know the original authors used dt = 1 fs, but the point > remains. > > -Justin > > > Nilesh Dhumal wrote: > >> Hello, >> >> >> I am using flexible water model for my system. I am referring a paper >> J. >> Chem. Phys. 124, 024503 (2006). Author have used Amber type force field. >> >> >> i.e. 1/2 Kbond (r-req)**2 + 1/2 Kangle(theta-thetaeq)**2. >> >> Kbond = 443153.3808 kJ/mol nm**2 >> >> >> Kangle= 317.5656 kJ/mol rad**2. >> >> >> I am using olss-aa force field parameters in Gromacs VERSION 4.0.7. >> >> >> I checked some papers in which author have used oplsaa force field in >> Gromacs. 1/2 factor is not in opls force field if I compare opls and >> amber. >> >> >> I didnt get the proper dielectric constant for water when I used the >> parameters reported in paper >> >> (Kbond = 443153.3808 kJ/mol nm**2,Kangle= 317.5656 kJ/mol rad**2) >> >> >> I half the value of Kb and get the proper dielectric constant (~80) for >> water reported in paper. If I half Kangle then I dont get proper >> value. Below are the results for the dielectric constant of water. >> Bond length is nm. >> >> >> Here I have done some analysis. The original value reported in J. >> Chem. >> Phys. 124, 024503 2006, paper are >> >> >> Kbond = 443153.3808 kJ/mol nm**2 >> Kangle = 317.5656 kJ/mol rad**2. >> >> >> >> bond lengthKbond angleKangledielectric constant >> 0.1012 >> 443153.3808113.24 317.5656 ~1.9 : orginal value >> >> >> >> 0.1012 221576.6904113.24 317.5656 ~80 : 1/2 (Kbond) >> >> >> >> 0.1012 443153.3808113.24 158.7828 ~1.58 : 1/2 (kangle) >> >> >> >> 0.1012 221576.6904113.24 317.5656 ~1.9 : 1/2 >> (Kbond)&(Kangle) >> >> >> >> Here I pasted spc_fw.itp file used for the simulation. >> >> >> ; Derived from parsing of runfiles/alat.top.orig >> [ defaults ] >> ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ >> ;1 3 yes 0.5 0.5 >> ; comb-rule 3 is square-root sigma, the OPLSAA version >> >> >> [ atomtypes ] >> ; full atom descriptions are available in ffoplsaa.atp >> ; name bond_typemasscharge ptype sigma epsilon >> opls_1001 OW 8 15.99940-0.820 A3.1655e-01 >&g
Re: [gmx-users] ambar to opls force field
I used g_dipoles to calculate dielectric constant. g_dipoles -f water.trr -s water.tpr -eps Group 0 ( System) has 768 elements Group 1 ( Protein) has 768 elements Group 2 ( Protein-H) has 256 elements Group 3 ( C-alpha) has 0 elements Group 4 (Backbone) has 0 elements Group 5 ( MainChain) has 0 elements Group 6 (MainChain+Cb) has 0 elements Group 7 ( MainChain+H) has 0 elements Group 8 ( SideChain) has 768 elements Group 9 ( SideChain-H) has 256 elements Select a group: 0 I selected 0. Nilesh On Mon, May 9, 2011 8:28 am, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Hello Justin, >> >> >> In the J. Chem. Phys. paper author have run the simulation 6.5 ns. So >> >> >> I run the simulation 6.5 ns for collecting data and I have total 256 >> water molecules. > > I also asked how you calculated the dielectric constant. > > > When trying to replicate others' work, it is often most beneficial and > less time-consuming to simply contact the corresponding author of the > paper. They can talk with you directly about methodological details. > > -Justin > > >> NIlesh >> >> >> On Sun, May 8, 2011 11:58 pm, Justin A. Lemkul wrote: >> >> >>> Nilesh Dhumal wrote: >>> >>> >>>> Hello Justin, >>>> >>>> >>>> >>>> Here I have done some analysis. The original value reported in >>>> J.Chem. >>>> Phys. 124, 024503 2006, paper are >>>> Kbond = 443153.3808 kJ/mol nm**2 >>>> Kangle = 317.5656 kJ/mol rad**2. >>>> >>>> >>>> >>>> >>>> Below are the results for the dielectric constant of water.I made >>>> the .itp >>>> file pasted below the table. Bond length is nm. >>>> >>>> bond length Kbond angleKangledielectric constant >>>> 0.1012 >>>> 443153.3808113.24 317.5656 ~1.9 : orginal value >>>> >>>> >>>> >>>> 0.1012 221576.6904113.24 317.5656 ~80 : 1/2 >>>> (Kbond) >>>> >>>> >>>> >>>> 0.1012 443153.3808113.24 158.7828 ~1.58 : 1/2 >>>> (kangle) >>>> >>>> >>>> >>>> 0.1012 221576.6904113.24 317.5656 ~1.9 : 1/2 >>>> (Kbond)&(Kangle) >>>> >>>> >>>> >>> How were these dielectric constants calculated? Did you collect >>> sufficient data? It seems to me that there is no definitive >>> dependence on any of these parameters, and you have one outlying point >>> that is coincidentally close to what you want. A consistently wrong >>> dielectric would suggest that either you're not calculating it right >>> or you don't have sufficiently converged data. >>> >>> Based on a quick look through the paper, it seems to me that your >>> original premise of converting between force fields is not related to >>> the task at hand. Water models are relatively force field-agnostic, >>> especially when trivial functional forms, such as harmonic potentials, >>> are applied. There is nothing >>> fancy here. >>> >>> Given the following: >>> >>> >>> >>>> [ bondtypes ] >>>> ; ij func b0 kb >>>> OWHW 10.1012 443153.3808 ; J. Chem. Phys. >>>> (2006),124,024503 >>>> [ angletypes ] >>>> ; ijk func th0 cth >>>> HW OW HW 1 113.24 158.7828 ; J. Chem. Phys. >>>> (2006),124,024503 >>>> >>>> >>>> >>> You are indeed applying simple harmonic potentials (see the manual to >>> confirm the form), which again indicates to me that you should not >>> be playing with the force constants in the model described in the >>> paper. Use Ka and Kb as listed. >>> Halving these quantities will result in a harmonic potential, e.g. for >>> bonds of (1/4)Kb(b-b0)^2 rather then the proper coefficient of 1/2. >>> >>> >>> -Justin >>> >>> >>> >>> -- >>> >>> >>> >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >&g
Re: [gmx-users] ambar to opls force field
Hello Justin, In the J. Chem. Phys. paper author have run the simulation 6.5 ns. So I run the simulation 6.5 ns for collecting data and I have total 256 water molecules. NIlesh On Sun, May 8, 2011 11:58 pm, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Hello Justin, >> >> >> Here I have done some analysis. The original value reported in J.Chem. >> Phys. 124, 024503 2006, paper are >> Kbond = 443153.3808 kJ/mol nm**2 >> Kangle = 317.5656 kJ/mol rad**2. >> >> >> >> Below are the results for the dielectric constant of water.I made the >> .itp >> file pasted below the table. Bond length is nm. >> >> bond length Kbond angleKangledielectric constant 0.1012 >> 443153.3808113.24 317.5656 ~1.9 : orginal value >> >> >> 0.1012 221576.6904113.24 317.5656 ~80 : 1/2 (Kbond) >> >> >> 0.1012 443153.3808113.24 158.7828 ~1.58 : 1/2 (kangle) >> >> >> 0.1012 221576.6904113.24 317.5656 ~1.9 : 1/2 >> (Kbond)&(Kangle) >> >> > > How were these dielectric constants calculated? Did you collect > sufficient data? It seems to me that there is no definitive dependence on > any of these parameters, and you have one outlying point that is > coincidentally close to what you want. A consistently wrong dielectric > would suggest that either you're not calculating it right or you don't > have sufficiently converged data. > > Based on a quick look through the paper, it seems to me that your > original premise of converting between force fields is not related to the > task at hand. Water models are relatively force field-agnostic, especially > when trivial functional forms, such as harmonic potentials, are applied. > There is nothing > fancy here. > > Given the following: > > >> [ bondtypes ] >> ; ij func b0 kb >> OWHW 10.1012 443153.3808 ; J. Chem. Phys. >> (2006),124,024503 >> [ angletypes ] >> ; ijk func th0 cth >> HW OW HW 1 113.24 158.7828 ; J. Chem. Phys. >> (2006),124,024503 >> >> > > You are indeed applying simple harmonic potentials (see the manual to > confirm the form), which again indicates to me that you should not be > playing with the force constants in the model described in the paper. Use > Ka and Kb as listed. > Halving these quantities will result in a harmonic potential, e.g. for > bonds of (1/4)Kb(b-b0)^2 rather then the proper coefficient of 1/2. > > > -Justin > > > -- > > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] ambar to opls force field
Hello Justin, Here I have done some analysis. The original value reported in J.Chem. Phys. 124, 024503 2006, paper are Kbond = 443153.3808 kJ/mol nm**2 Kangle = 317.5656 kJ/mol rad**2. Below are the results for the dielectric constant of water.I made the .itp file pasted below the table. Bond length is nm. bond length Kbond angleKangledielectric constant 0.1012 443153.3808113.24 317.5656 ~1.9 : orginal value 0.1012 221576.6904113.24 317.5656 ~80 : 1/2 (Kbond) 0.1012 443153.3808113.24 158.7828 ~1.58 : 1/2 (kangle) 0.1012 221576.6904113.24 317.5656 ~1.9 : 1/2 (Kbond)&(Kangle) When I use half Kbond value I get proper dielectic constant for water (~80). I checked the Kbond for OH in opls force field is around ~ 44. I don't now where I am going wrong. Here I pasted spc_fw.itp file ; Derived from parsing of runfiles/alat.top.orig [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_1001 OW 8 15.99940-0.820 A3.1655e-01 6.503e-01 opls_1002 HW 1 1.00800 0.410 A0.00e+00 0.00e+00 [ bondtypes ] ; ij func b0 kb OWHW 10.1012 443153.3808 ; J. Chem. Phys. (2006),124,024503 [ angletypes ] ; ijk func th0 cth HW OW HW 1 113.24 158.7828 ; J. Chem. Phys. (2006),124,024503 [ moleculetype ] ; Namenrexcl WAT 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_1001 1WAT OW 1 -0.82 15.99940 ; 2 opls_1002 1WATHW1 1 0.41 1.008 ; 3 opls_1002 1WATHW2 1 0.41 1.008 ; [ bonds ] ; i j funct 1 2 1 1 3 1 [ angles ] ; i j k funct 2 1 3 1 In water.top file, I included spc_fw.itp file. ; Include water topology #include "spc_fw.itp" Is there any thing worng in .itp file or where I am making mistake. Thanks Nilesh On Sun, May 8, 2011 10:55 am, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Thanks Justin. >> >> >> I am using flexibale water model for my system. I am refering a paper >> J. >> Chem. Phys. 124, 024503 (2006). Author have used Amber type force field. >> >> >> i.e. 1/2 Kbond (r-req)**2 + 1/2 Kangle(theta-thetaeq)**2. >> >> Kbond = 443153.3808 kJ/mol nm**2 >> >> >> Kangle= 317.5656 kJ/mol rad**2. >> >> >> I am using olss-aa force field parameters in Gromacs VERSION 4.0.7. >> >> >> I checked some papers in which author have used opls aa force field. >> 1/2 >> factor is not in opls force field IF I compare opls and amber. >> >> My question is in .itp file should I use Kbond and Kangle as it is or >> should I consider the 1/2 factor then I use them. >> > > Both of those terms are simple harmonic expressions, which do not require > any modification. Per the manual, Gromacs uses these expressions as is, > so Kb and Ka should be appropriate as listed. They are of comparable > magnitude to existing bonded parameters for such terms. > > You can, of course, test this by using the same parameters under the > original AMBER force field used in the paper you cite, and then again > after incorporation into the OPLS-AA force field. If the resulting > averages are the same, then the new parameters have been incorporated > correctly. > > -Justin > > >> Thanks >> >> >> Nilesh >> >> >> On Fri, May 6, 2011 6:36 pm, Justin A. Lemkul wrote: >> >> >>> Nilesh Dhumal wrote: >>> >>> >>>> Hello, >>>> >>>> >>>> >>>> How can I convert ambar force field to opls force field. >>>> >>>> >>>> >>>> Should I half the force constant of bond (Ka) and angle (Kb)? >>>> >>>> >>>> >>> Why would you do that? Most of the bonded parameters in OPLS were >>> taken from AMBER directly, IIRC. If you need to parameterize some new >>> bonded parameters, you'd be better served deriving them in a way that >>> is compatible with the modern OPLS-AA force field (probably >>> QM/geometry >>> optimization), rather than trying to hack something together. >>> >>> -Justin >
Re: [gmx-users] ambar to opls force field
Thanks Justin. I am using flexibale water model for my system. I am refering a paper J. Chem. Phys. 124, 024503 (2006). Author have used Amber type force field. i.e. 1/2 Kbond (r-req)**2 + 1/2 Kangle(theta-thetaeq)**2. Kbond = 443153.3808 kJ/mol nm**2 Kangle= 317.5656 kJ/mol rad**2. I am using olss-aa force field parameters in Gromacs VERSION 4.0.7. I checked some papers in which author have used opls aa force field. 1/2 factor is not in opls force field IF I compare opls and amber. My question is in .itp file should I use Kbond and Kangle as it is or should I consider the 1/2 factor then I use them. Thanks Nilesh On Fri, May 6, 2011 6:36 pm, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Hello, >> >> >> How can I convert ambar force field to opls force field. >> >> >> Should I half the force constant of bond (Ka) and angle (Kb)? >> >> > > Why would you do that? Most of the bonded parameters in OPLS were taken > from AMBER directly, IIRC. If you need to parameterize some new bonded > parameters, you'd be better served deriving them in a way that is > compatible with the modern OPLS-AA force field (probably QM/geometry > optimization), rather than trying to hack something together. > > -Justin > > > -- > > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] ambar to opls force field
Hello, How can I convert ambar force field to opls force field. Should I half the force constant of bond (Ka) and angle (Kb)? NIlesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] constraints
Hello, In my input file if I don't specify "constraints" then What is default constraints=none constraints=all bonds NIlesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] flexiable water - model
I have total 256 water molecules. I am trying to genrate the .top file from .pdb so I used pdb2gmx. How can I genrate the .top file with pdb2gmx for 256 water molecules. Nilesh On Tue, April 26, 2011 1:01 pm, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Hello, >> >> >> I am trying to run a simulation for flexiable water. I use the >> parameters from J. Chem. Phys. (2006),124,024503 paper and made floowing >> changes. >> >> I addes "WAT" as a new residue name in aminoacids.dat >> >> >> I addred two atom times in ffoplsaa.atp >> >> >> opls_1001 15.99940 ; O SPC_fw Water opls_10021.00800 ; H SPC_fw >> Water >> >> >> >> I added following parameters in ffoplsaa.rtp >> >> >> [ WAT] >> [ atoms ] >> OWA opls_1001 -0.82 1 >> HWA1 opls_1002 0.41 2 >> HWA2 opls_1002 0.41 2 >> >> >> [ bonds ] >> OWA HWA1 >> OWA HWA2 >> >> >> I made a spc_fw.itp file. >> >> >> ; Derived from parsing of runfiles/alat.top.orig >> [ defaults ] >> ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ >> ;1 3 yes 0.5 0.5 >> ; comb-rule 3 is square-root sigma, the OPLSAA version >> >> >> [ atomtypes ] >> ; full atom descriptions are available in ffoplsaa.atp >> ; name bond_typemasscharge ptype sigma epsilon >> opls_1001 OWA 815.99940 -0.820 A3.1655e-01 >> 6.503e-01 >> opls_1002 HWA 1 1.00800 0.410 A0.00e+00 0.00e+00 >> >> [ bondtypes ] >> ; ij func b0 kb >> OWAHWA 10.1012 443153.3808 ; J. Chem. Phys. >> (2006),124,024503 >> >> >> >> [ angletypes ] >> ; ijk func th0 cth >> HWA OWA HWA 1 113.24 317.5656 ; J. Chem. Phys. >> (2006),124,024503 >> >> >> [ moleculetype ] >> ; Namenrexcl >> WAT 3 >> >> >> [ atoms ] >> >> >> ; nr type resnr residue atom cgnr charge mass >> typeB chargeB massB 1 opls_1001 1WAT OWA 1 >> -0.82 >> 2 opls_1002 1WATHWA1 1 0.41 >> 3 opls_1002 1WATHWA2 1 0.41 >> >> >> [ bonds ] >> ; i j funct >> 1 2 1 >> 1 3 1 >> >> >> >> [ angles ] >> ; i j k funct >> 2 1 3 1 >> >> >> >> Finally I made changes in ffoplsaa.itp file >> >> >> ;#include "ffoplsaanb.itp" >> ;#include "ffoplsaabon.itp" >> #include "spc_fw.itp" >> #include "spc_fw_mol.itp" >> >> >> For pdb2gmx >> >> >> pdb2gmx -f water.pdb -o water.pdb -p water.top -ter >> >> I get following error >> >> >> Fatal error: >> Atom OWA in residue HOH 1 not found in rtp entry with 3 atoms >> while sorting atoms >> >> >> WHy is reading HOH residue. In my pdb file I mentioned WAT as residure. >> >> >> How can I fix this error? >> >> > > If I recall, pdb2gmx does some internal translations to standardize water > nomenclature. In reality, you don't need pdb2gmx at all - you've > already shown that you're created a topology for the water model. > > -Justin > > > -- > > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] flexiable water - model
Hello, I am trying to run a simulation for flexiable water. I use the parameters from J. Chem. Phys. (2006),124,024503 paper and made floowing changes. I addes "WAT" as a new residue name in aminoacids.dat I addred two atom times in ffoplsaa.atp opls_1001 15.99940 ; O SPC_fw Water opls_10021.00800 ; H SPC_fw Water I added following parameters in ffoplsaa.rtp [ WAT] [ atoms ] OWA opls_1001 -0.82 1 HWA1 opls_1002 0.41 2 HWA2 opls_1002 0.41 2 [ bonds ] OWA HWA1 OWA HWA2 I made a spc_fw.itp file. ; Derived from parsing of runfiles/alat.top.orig [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_1001 OWA 815.99940 -0.820 A3.1655e-01 6.503e-01 opls_1002 HWA 1 1.00800 0.410 A0.00e+00 0.00e+00 [ bondtypes ] ; ij func b0 kb OWAHWA 10.1012 443153.3808 ; J. Chem. Phys. (2006),124,024503 [ angletypes ] ; ijk func th0 cth HWA OWA HWA 1 113.24 317.5656 ; J. Chem. Phys. (2006),124,024503 [ moleculetype ] ; Namenrexcl WAT 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_1001 1WAT OWA 1 -0.82 2 opls_1002 1WATHWA1 1 0.41 3 opls_1002 1WATHWA2 1 0.41 [ bonds ] ; i j funct 1 2 1 1 3 1 [ angles ] ; i j k funct 2 1 3 1 Finally I made changes in ffoplsaa.itp file ;#include "ffoplsaanb.itp" ;#include "ffoplsaabon.itp" #include "spc_fw.itp" #include "spc_fw_mol.itp" For pdb2gmx pdb2gmx -f water.pdb -o water.pdb -p water.top -ter I get following error Fatal error: Atom OWA in residue HOH 1 not found in rtp entry with 3 atoms while sorting atoms WHy is reading HOH residue. In my pdb file I mentioned WAT as residure. How can I fix this error? Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
