[gmx-users] Re: single point calculation with gromacs
Dear Justin, *Thanks very much for your reply! Here is my minim.mdp I used:* /; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 0 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = simple; Method to determine neighbor list (simple, grid) rlist = 9.0 ; Cut-off for making neighbor list (short range forces) coulombtype = Cut-off ; Treatment of long range electrostatic interactions rcoulomb= 9.0 ; Short-range electrostatic cut-off rvdw= 9.0 ; Short-range Van der Waals cut-off pbc = no; Periodic Boundary Conditions (yes/no) / *If I used this mdp file for 0-step minimization, I could get potential energy around 700 kJ/mol for my system. But I would get potential energy around 2.6e+05 kJ/mol if I used the mdv.mdp (md simulation in vacuum) for calculations with rerun option. And the bond potential could also reach as high as 1.1e+05 kJ/mol. Actually, my system is very small, it contains only 37 atoms. I believe that the energy reported by 0-step minimization were more reasonable. So I guess that there might be some problem for the mdp file usd with rerun, and here is the mdv.mdp:* /define = ;-DPOSRES integrator = md ; molecular dynamics algorithm tinit = 0.0 ; start time and timestep in ps dt = 0.002; time step in ps nsteps = 2; number of steps for 1000ns run emtol = 100; convergence criterion emstep = 0.05 ; intial step size nstlist = 0 ; step frequency for updating neighbour list ns_type = simple ; method for neighbour searching (?) nstxout = 1; frequency for writing coords to output .trr file nstvout = 1 ; frequency for writing velocities to output...should be same as nstxout nstfout = 1; frequency for writing forces to output nstlog = 1 ; frequency for writing energies to log file nstenergy = 1 ; frequency for writing energies to energy file nstxtcout = 1 ; frequency for writing coords to xtc traj xtc_grps= system ; group(s) whose coords are to be written in xtc traj energygrps = system ; group(s) whose energy is to be written in energy file pbc = no ; use pbc rlist = 0 ; cutoff lengths (nm) epsilon_r = 1.0 ; Dielectric constant (DC) for twin-range or DC of reaction field niter = 100 ; Some thingies for future use fourierspacing = 0.16 fourier_nx = 30 fourier_ny = 30 fourier_nz = 30 coulombtype = Cut-off ; truncation for minimisation, with large cutoff rcoulomb= 0 rcoulomb-switch = 0 vdw-type = Cut-off ; truncation for minimisation, with large cutoff rvdw-switch = 0 rvdw = 0 ; cut-off lengths epsilon_surface = 0 optimize_fft = yes Tcoupl = V-rescale tc_grps = system tau_t = 0.01 ref_t = 300 Pcoupl = no ; Parrinello-Rahman ; Pressure coupling gen_vel = yes gen_temp= 300 gen_seed= -1 constraints = none ; OPTIONS FOR BOND CONSTRAINTS constraint-algorithm = Lincs ; Type of constraint algorithm lincs_order = 4;4; Highest order in the expansion of the constraint coupling matrix lincs_iter = 1 lincs_warnangle = 30 ; Lincs will write a warning to the stderr if in one step a bond rotates ; over more degrees than unconstrained-start = no ; Do not constrain the start configuration ;Shake-SOR= no ; Use successive overrelaxation to reduce the number of shake iterations ;shake-tol= 1e-04 ; Relative tolerance of shake morse= no ; Convert harmonic bonds to morse potentials / *Could you please have a check for me again? Thanks in advance! All the best, Qinghua* -- View this message in context: http://gromacs.5086.x6.nabble.com/single-point-calculation-with-gromacs-tp5012084p5012100.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list
[gmx-users] Re: single point calculation with gromacs
Dear Justin, *Thanks very much for your reply! Here is my minim.mdp I used:* /; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 0 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = simple; Method to determine neighbor list (simple, grid) rlist = 9.0 ; Cut-off for making neighbor list (short range forces) coulombtype = Cut-off ; Treatment of long range electrostatic interactions rcoulomb= 9.0 ; Short-range electrostatic cut-off rvdw= 9.0 ; Short-range Van der Waals cut-off pbc = no; Periodic Boundary Conditions (yes/no) / *If I used this mdp file for 0-step minimization, I could get potential energy around 700 kJ/mol for my system. But I would get potential energy around 2.6e+05 kJ/mol if I used the mdv.mdp (md simulation in vacuum) for calculations with rerun option. And the bond potential could also reach as high as 1.1e+05 kJ/mol. Actually, my system is very small, it contains only 37 atoms. I believe that the energy reported by 0-step minimization were more reasonable. So I guess that there might be some problem for the mdp file usd with rerun, and here is the mdv.mdp:* /define = ;-DPOSRES integrator = md ; molecular dynamics algorithm tinit = 0.0 ; start time and timestep in ps dt = 0.002; time step in ps nsteps = 2; number of steps for 1000ns run emtol = 100; convergence criterion emstep = 0.05 ; intial step size nstlist = 0 ; step frequency for updating neighbour list ns_type = simple ; method for neighbour searching (?) nstxout = 1; frequency for writing coords to output .trr file nstvout = 1 ; frequency for writing velocities to output...should be same as nstxout nstfout = 1; frequency for writing forces to output nstlog = 1 ; frequency for writing energies to log file nstenergy = 1 ; frequency for writing energies to energy file nstxtcout = 1 ; frequency for writing coords to xtc traj xtc_grps= system ; group(s) whose coords are to be written in xtc traj energygrps = system ; group(s) whose energy is to be written in energy file pbc = no ; use pbc rlist = 0 ; cutoff lengths (nm) epsilon_r = 1.0 ; Dielectric constant (DC) for twin-range or DC of reaction field niter = 100 ; Some thingies for future use fourierspacing = 0.16 fourier_nx = 30 fourier_ny = 30 fourier_nz = 30 coulombtype = Cut-off ; truncation for minimisation, with large cutoff rcoulomb= 0 rcoulomb-switch = 0 vdw-type = Cut-off ; truncation for minimisation, with large cutoff rvdw-switch = 0 rvdw = 0 ; cut-off lengths epsilon_surface = 0 optimize_fft = yes Tcoupl = V-rescale tc_grps = system tau_t = 0.01 ref_t = 300 Pcoupl = no ; Parrinello-Rahman ; Pressure coupling gen_vel = yes gen_temp= 300 gen_seed= -1 constraints = none ; OPTIONS FOR BOND CONSTRAINTS constraint-algorithm = Lincs ; Type of constraint algorithm lincs_order = 4;4; Highest order in the expansion of the constraint coupling matrix lincs_iter = 1 lincs_warnangle = 30 ; Lincs will write a warning to the stderr if in one step a bond rotates ; over more degrees than unconstrained-start = no ; Do not constrain the start configuration ;Shake-SOR= no ; Use successive overrelaxation to reduce the number of shake iterations ;shake-tol= 1e-04 ; Relative tolerance of shake morse= no ; Convert harmonic bonds to morse potentials / *Could you please have a check for me again? Thanks in advance! All the best, Qinghua* -- View this message in context: http://gromacs.5086.x6.nabble.com/single-point-calculation-with-gromacs-tp5012084p5012101.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list
[gmx-users] Re: gmx-users Digest, Vol 114, Issue 91
On 10/30/13 11:26 AM, Knapp Bernhard wrote: Hi users, I was wondering if there is an easy and quick way to get a frame-wise binding energy between 2 groups of chains (chain ABC vs DE) in an existing trajectory. This is not indented to be an actual binding free energy approach but rather a rough indicator if the binding between two chains increases or decreases during simulation time. This should work like a protein/protein docking scoring function which assigns binding scores to single conformations. Is there a direct approach on an existing xtc (even if water was removed and not all steps were written)? Maybe like g_hbond but in addition with terms like Gvdw, Gdeformation, Ghydrophobic etc. Alternatively (and probably much more time and resource consuming), would it be possible to obtain this by the rerun option of mdrun (adjusted energy monitoring groups (the original setup was energygrps = proteinSOL))? Using energygrps is the closest you'll get without modifying the code. You'll get decomposed short-range nonbonded terms, which can perhaps provide some indicator of the strength of the interaction between the two entities. -Justin Hmm ok if Gromacs does not provide something like this then I ask the question a little bit different: Does someone know a pure scoring function for protein/protein interaction? It should not be a complete docking program but rather something which can simply evaluate given conformations (coming from an MD trajectory) ... and it should also not be a webserver (like ClusPro) but a downloadable binary because I want to test a quite high amount of conformations. Something like XSCORE [J Comp Aid Des, 16: 11-26. 2002] but instead of ligand/protein for protein/protein interactions. Cheers, Bernhard -- 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] RNA simulation
Hi I'm going to study the molecular dynamics of an RNA(which has stem-loop structure) by comparison the native RNA structure and it's mutant to find the conformation changes of 3D structure. This RNA comprises 70 nucleotides. Do you think that it would be possible in Gromacs. -- 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: single point calculation with gromacs
On 10/31/13 4:57 AM, fantasticqhl wrote: Dear Justin, *Thanks very much for your reply! Here is my minim.mdp I used:* /; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 0 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = simple; Method to determine neighbor list (simple, grid) rlist = 9.0 ; Cut-off for making neighbor list (short range forces) coulombtype = Cut-off ; Treatment of long range electrostatic interactions rcoulomb= 9.0 ; Short-range electrostatic cut-off rvdw= 9.0 ; Short-range Van der Waals cut-off pbc = no; Periodic Boundary Conditions (yes/no) / *If I used this mdp file for 0-step minimization, I could get potential energy around 700 kJ/mol for my system. But I would get potential energy around 2.6e+05 kJ/mol if I used the mdv.mdp (md simulation in vacuum) for calculations with rerun option. And the bond potential could also reach as high as 1.1e+05 kJ/mol. Actually, my system is very small, it contains only 37 atoms. I believe that the energy reported by 0-step minimization were more reasonable. So I guess that there might be some problem for the mdp file usd with rerun, and here is the mdv.mdp:* /define = ;-DPOSRES integrator = md ; molecular dynamics algorithm tinit = 0.0 ; start time and timestep in ps dt = 0.002; time step in ps nsteps = 2; number of steps for 1000ns run emtol = 100; convergence criterion emstep = 0.05 ; intial step size nstlist = 0 ; step frequency for updating neighbour list ns_type = simple ; method for neighbour searching (?) nstxout = 1; frequency for writing coords to output .trr file nstvout = 1 ; frequency for writing velocities to output...should be same as nstxout nstfout = 1; frequency for writing forces to output nstlog = 1 ; frequency for writing energies to log file nstenergy = 1 ; frequency for writing energies to energy file nstxtcout = 1 ; frequency for writing coords to xtc traj xtc_grps= system ; group(s) whose coords are to be written in xtc traj energygrps = system ; group(s) whose energy is to be written in energy file pbc = no ; use pbc rlist = 0 ; cutoff lengths (nm) epsilon_r = 1.0 ; Dielectric constant (DC) for twin-range or DC of reaction field niter = 100 ; Some thingies for future use fourierspacing = 0.16 fourier_nx = 30 fourier_ny = 30 fourier_nz = 30 coulombtype = Cut-off ; truncation for minimisation, with large cutoff rcoulomb= 0 rcoulomb-switch = 0 vdw-type = Cut-off ; truncation for minimisation, with large cutoff rvdw-switch = 0 rvdw = 0 ; cut-off lengths epsilon_surface = 0 optimize_fft = yes Tcoupl = V-rescale tc_grps = system tau_t = 0.01 ref_t = 300 Pcoupl = no ; Parrinello-Rahman ; Pressure coupling gen_vel = yes gen_temp= 300 gen_seed= -1 constraints = none ; OPTIONS FOR BOND CONSTRAINTS constraint-algorithm = Lincs ; Type of constraint algorithm lincs_order = 4;4; Highest order in the expansion of the constraint coupling matrix lincs_iter = 1 lincs_warnangle = 30 ; Lincs will write a warning to the stderr if in one step a bond rotates ; over more degrees than unconstrained-start = no ; Do not constrain the start configuration ;Shake-SOR= no ; Use successive overrelaxation to reduce the number of shake iterations ;shake-tol= 1e-04 ; Relative tolerance of shake morse= no ; Convert harmonic bonds to morse potentials / *Could you please have a check for me again? Thanks in advance! Was anything in the bug report I posted before relevant? If you're using any version in the 4.6.x series, you may be observing some of the same behavior I did. There are numerous differences between these .mdp
[gmx-users] cool down problem
Dear all, I'm having some problems during the cool-down process after the NVT. I'm running the NVT process at a T of 500K for 3ns and everything is going well but when I cool down the system blows up. I am running the cool down for 100ps, I tried to run the process for longer time (500 ps) and decrease nstlist option up to 5 but it seems it doesn't work. The EM seems to be fine with very low forces: Potential Energy = -3.1736706e+05 Maximum force = 2.6573439e+01 on atom 105 Norm of force = 3.1027287e-01 The NVT is compiled with the following mdp: define = -DPOSRES ; position restrain the protein and ligand ; Run parameters integrator = md; leap-frog integrator nsteps = 150 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 1 ; save coordinates every 0.2 ps nstvout = 1 ; save velocities every 0.2 ps nstenergy = 1 ; save energies every 0.2 ps nstlog = 1 ; update log file every 0.2 ps energygrps = NAP NA WAT MET SI3 SI- I LI+ LI- ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching vdwtype = cutoff ns_type = grid ; search neighboring grid cells nstlist = 20 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = NAP NA WAT MET SI3 SI- I LI+ LI- ; two coupling groups - more accurate tau_t = 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 ; time constant, in ps ref_t = 500 500 500 500 500 500 500 500 500 ; reference temperature, one for each group, in K ; Pressure coupling pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 298 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed The cooldown mdp is the following: integrator = md tinit= 0 dt = 0.001 nsteps = 10; 100 ps simulation_part = 1 init_step= 0 comm-mode= Linear nstcomm = 1 comm-grps= bd-fric = 0 ld-seed = 1993 rtpi = 0.05 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 500 nstenergy= 100 nstxtcout= 500 xtc-precision= 1000 xtc-grps = nstlist = 10 ns_type = grid pbc = xyz periodic_molecules = no rlist= 0.9 coulombtype = PME rcoulomb-switch = 0 rcoulomb = 0.9 epsilon_r= 1 epsilon_rf = 1 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.0 DispCorr = No table-extension = 1 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 6 ewald_rtol = 1e-5 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = yes gb_algorithm = Still nstgbradii = 1 rgbradii = 2 gb_epsilon_solvent = 80 gb_saltconc = 0 OBC(II) gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 sa_surface_tension = 2.092 Tcoupl = v-rescale tc-grps = system tau_t= 0.1 ref_t= 1000 Pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p= 2 compressibility = 4.5e-5 ref_p= 1 refcoord_scaling = No andersen_seed= 815131 annealing= single annealing_npoints= 2 annealing_time = 0 80 annealing_temp = 500 298 gen_vel = no gen_temp = 500 gen_seed =
Re: [gmx-users] cool down problem
On 10/31/13 8:25 AM, Riccardo Concu wrote: Dear all, I'm having some problems during the cool-down process after the NVT. I'm running the NVT process at a T of 500K for 3ns and everything is going well but when I cool down the system blows up. I am running the cool down for 100ps, I tried to run the process for longer time (500 ps) and decrease nstlist option up to 5 but it seems it doesn't work. The EM seems to be fine with very low forces: Potential Energy = -3.1736706e+05 Maximum force = 2.6573439e+01 on atom 105 Norm of force = 3.1027287e-01 The NVT is compiled with the following mdp: define = -DPOSRES ; position restrain the protein and ligand ; Run parameters integrator = md; leap-frog integrator nsteps = 150 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 1 ; save coordinates every 0.2 ps nstvout = 1 ; save velocities every 0.2 ps nstenergy = 1 ; save energies every 0.2 ps nstlog = 1 ; update log file every 0.2 ps energygrps = NAP NA WAT MET SI3 SI- I LI+ LI- ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching vdwtype = cutoff ns_type = grid ; search neighboring grid cells nstlist = 20 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = NAP NA WAT MET SI3 SI- I LI+ LI- ; two coupling groups - more accurate Frankly, I'm amazed this was stable. I can't imagine that any system justifies this many individual thermostats. snip Pcoupl = Parrinello-Rahman I doubt that you want to try to use Parrinello-Rahman while simultaneously decreasing the temperature. Even for equilibration runs at stable temperature, P-R is a poor choice. I would suggest trying your cooling under NVT, or if you absolutely need to do it under NPT, use Berendsen instead; it is much more forgiving. -Justin -- == 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.edu | (410) 706-7441 == -- 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-users Digest, Vol 114, Issue 91
I think ProDy can do this. It is a python module for analysis of structures that can be downloaded from http://www.csb.pitt.edu/ProDy/ I'm not sure it can read xtc but you can probably use it after converting trajectories to pdb. On 10/30/13 11:26 AM, Knapp Bernhard wrote: Hi users, I was wondering if there is an easy and quick way to get a frame-wise binding energy between 2 groups of chains (chain ABC vs DE) in an existing trajectory. This is not indented to be an actual binding free energy approach but rather a rough indicator if the binding between two chains increases or decreases during simulation time. This should work like a protein/protein docking scoring function which assigns binding scores to single conformations. Is there a direct approach on an existing xtc (even if water was removed and not all steps were written)? Maybe like g_hbond but in addition with terms like Gvdw, Gdeformation, Ghydrophobic etc. Alternatively (and probably much more time and resource consuming), would it be possible to obtain this by the rerun option of mdrun (adjusted energy monitoring groups (the original setup was energygrps = proteinSOL))? Using energygrps is the closest you'll get without modifying the code. You'll get decomposed short-range nonbonded terms, which can perhaps provide some indicator of the strength of the interaction between the two entities. -Justin Hmm ok if Gromacs does not provide something like this then I ask the question a little bit different: Does someone know a pure scoring function for protein/protein interaction? It should not be a complete docking program but rather something which can simply evaluate given conformations (coming from an MD trajectory) ... and it should also not be a webserver (like ClusPro) but a downloadable binary because I want to test a quite high amount of conformations. Something like XSCORE [J Comp Aid Des, 16: 11-26. 2002] but instead of ligand/protein for protein/protein interactions. Cheers, Bernhard -- 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] 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
Re: [gmx-users] Grompp note
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.edu | (410) 706-7441 == -- 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] cool down problem
Dear Justin, I ran a short simulation (200ps) with the cool down under NVT and now it seems the system is working. In addition, I removed from the NVT options the tc for all the groups. Thank you, Riccardo El jue, 31-10-2013 a las 08:31 -0400, Justin Lemkul escribió: On 10/31/13 8:25 AM, Riccardo Concu wrote: Dear all, I'm having some problems during the cool-down process after the NVT. I'm running the NVT process at a T of 500K for 3ns and everything is going well but when I cool down the system blows up. I am running the cool down for 100ps, I tried to run the process for longer time (500 ps) and decrease nstlist option up to 5 but it seems it doesn't work. The EM seems to be fine with very low forces: Potential Energy = -3.1736706e+05 Maximum force = 2.6573439e+01 on atom 105 Norm of force = 3.1027287e-01 The NVT is compiled with the following mdp: define = -DPOSRES ; position restrain the protein and ligand ; Run parameters integrator = md; leap-frog integrator nsteps = 150 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 1 ; save coordinates every 0.2 ps nstvout = 1 ; save velocities every 0.2 ps nstenergy = 1 ; save energies every 0.2 ps nstlog = 1 ; update log file every 0.2 ps energygrps = NAP NA WAT MET SI3 SI- I LI+ LI- ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching vdwtype = cutoff ns_type = grid ; search neighboring grid cells nstlist = 20 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = NAP NA WAT MET SI3 SI- I LI+ LI- ; two coupling groups - more accurate Frankly, I'm amazed this was stable. I can't imagine that any system justifies this many individual thermostats. snip Pcoupl = Parrinello-Rahman I doubt that you want to try to use Parrinello-Rahman while simultaneously decreasing the temperature. Even for equilibration runs at stable temperature, P-R is a poor choice. I would suggest trying your cooling under NVT, or if you absolutely need to do it under NPT, use Berendsen instead; it is much more forgiving. -Justin -- == 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.edu | (410) 706-7441 == -- 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 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.edu | (410) 706-7441 == -- 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] Grompp note
On 10/31/13 11:40 AM, Nilesh Dhumal wrote: 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. The relationship between high-frequency vibrations and the chosen timestep is a fundamental point in MD simulations. Any textbook covers it. There are even a few hints in the Gromacs manual. -Justin 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.edu | (410) 706-7441 == -- 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. 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
[gmx-users] No group in index file?
Dear all. Since I am interested in finding the average angle, dihedrals in my system, I attempted to use g_angle, but then I realized I need to make index file using mk_angndx, I issued the following: mk_angndx -s npt.tpr -n angle.ndx and then i used g_angle -f not.xtc -n angle.ndx -ov angle.xvg -noperiodic -type angle and then I get the following error: Fatal error: Error: no groups in indexfile How can my index file not have the groups in there? How can I go about fixing this Any insight can be appreciated Thanks, Xu Huang-- 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 group in index file?
On 10/31/13 1:36 PM, Xu Dong Huang wrote: Dear all. Since I am interested in finding the average angle, dihedrals in my system, I attempted to use g_angle, but then I realized I need to make index file using mk_angndx, I issued the following: mk_angndx -s npt.tpr -n angle.ndx and then i used g_angle -f not.xtc -n angle.ndx -ov angle.xvg -noperiodic -type angle and then I get the following error: Fatal error: Error: no groups in indexfile How can my index file not have the groups in there? How can I go about fixing this Inspect it with a text editor and/or gmxcheck. -Justin -- == 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.edu | (410) 706-7441 == -- 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] All-bonds vs. H-bonds using CHARMM36
Hi, In the CHARMM36 paper (Klauda et al., JPCB 2010), only the hydrogen bonds are constrained for the lipid simulations using SHAKE (excerpt from the paper below) Consistent for all of these simulations was the use of a 1 fs time step and constraining of the hydrogen atoms using the SHAKE algorithm. For a membrane-protein system, is constraining all-bonds via LINCS the right option while using CHARMM36? There was a mention somewhere (I forgot) that constraining all-bonds probably prevents alkane isomerisations in membranes, which could lower the melting temperature. I intend to simulate a POPC bilayer. Can someone with experience please shed some light on this? P.S.: Klauda et al., has posted their .mdp for POPE in gromacs on lipidbook. Their .mdp constrains h-bonds http://lipidbook.bioch.ox.ac.uk/uploads/package/CHARMM36/48-POPE-wurl/v1/charmm_npt.mdp Thank you. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] problem vwith ethanol-water solution
Hi gmx users, I want to solvate nafion molecules in a 3:1 ethanol water solution. I used genbox with -ci option to add ethanol to water when generating the box, but it did not work. Then, first I solvated the ethanol in water, and then added the nafion to the system, but these 3 molecules each sit a part from each other in the box in the pdb file. Any suggestion? Kind regards, Ehsan -- 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] problem vwith ethanol-water solution
Dear Ehsan, Did you try to pack your box with packmol? I have a similar system and packmol pack my system quite well and in a random way. Regards, Riccardo -Original Message- From: Ehsan Sadeghi Sent: Thursday, October 31, 2013 7:25 PM To: Discussion list for GROMACS users Subject: [gmx-users] problem vwith ethanol-water solution Hi gmx users, I want to solvate nafion molecules in a 3:1 ethanol water solution. I used genbox with -ci option to add ethanol to water when generating the box, but it did not work. Then, first I solvated the ethanol in water, and then added the nafion to the system, but these 3 molecules each sit a part from each other in the box in the pdb file. Any suggestion? Kind regards, Ehsan -- 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] No group in index file?
Dear all, so after I opened angle.ndx file in a text editor, the file appears to be blank. How can I properly make a index file since the command I issued seems to produce a blank index file? Is there something wrong with my input regarding npt.tpr? Thanks for your input, Xu Huang On Oct 31, 2013, at 1:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/31/13 1:36 PM, Xu Dong Huang wrote: Dear all. Since I am interested in finding the average angle, dihedrals in my system, I attempted to use g_angle, but then I realized I need to make index file using mk_angndx, I issued the following: mk_angndx -s npt.tpr -n angle.ndx and then i used g_angle -f not.xtc -n angle.ndx -ov angle.xvg -noperiodic -type angle and then I get the following error: Fatal error: Error: no groups in indexfile How can my index file not have the groups in there? How can I go about fixing this Inspect it with a text editor and/or gmxcheck. -Justin -- == 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.edu | (410) 706-7441 == -- 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] No group in index file?
Dear Xu, you have to use the make_ndx option if I'm not wrong. The syntax should be make_ndx -f xxx.gro -o index.ndx Cheers, -Original Message- From: Xu Dong Huang Sent: Thursday, October 31, 2013 8:52 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] No group in index file? Dear all, so after I opened angle.ndx file in a text editor, the file appears to be blank. How can I properly make a index file since the command I issued seems to produce a blank index file? Is there something wrong with my input regarding npt.tpr? Thanks for your input, Xu Huang On Oct 31, 2013, at 1:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/31/13 1:36 PM, Xu Dong Huang wrote: Dear all. Since I am interested in finding the average angle, dihedrals in my system, I attempted to use g_angle, but then I realized I need to make index file using mk_angndx, I issued the following: mk_angndx -s npt.tpr -n angle.ndx and then i used g_angle -f not.xtc -n angle.ndx -ov angle.xvg -noperiodic -type angle and then I get the following error: Fatal error: Error: no groups in indexfile How can my index file not have the groups in there? How can I go about fixing this Inspect it with a text editor and/or gmxcheck. -Justin -- == 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.edu | (410) 706-7441 == -- 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] No group in index file?
On 10/31/13 3:52 PM, Xu Dong Huang wrote: Dear all, so after I opened angle.ndx file in a text editor, the file appears to be blank. How can I properly make a index file since the command I issued seems to produce a blank index file? Is there something wrong with my input regarding npt.tpr? What version of Gromacs are you using? With 4.6.3, I get sensible output. -Justin Thanks for your input, Xu Huang On Oct 31, 2013, at 1:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/31/13 1:36 PM, Xu Dong Huang wrote: Dear all. Since I am interested in finding the average angle, dihedrals in my system, I attempted to use g_angle, but then I realized I need to make index file using mk_angndx, I issued the following: mk_angndx -s npt.tpr -n angle.ndx and then i used g_angle -f not.xtc -n angle.ndx -ov angle.xvg -noperiodic -type angle and then I get the following error: Fatal error: Error: no groups in indexfile How can my index file not have the groups in there? How can I go about fixing this Inspect it with a text editor and/or gmxcheck. -Justin -- == 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.edu | (410) 706-7441 == -- 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. 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.edu | (410) 706-7441 == -- 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 group in index file?
On 10/31/13 3:59 PM, Riccardo Concu wrote: Dear Xu, you have to use the make_ndx option if I'm not wrong. The syntax should be make_ndx -f xxx.gro -o index.ndx make_ndx is not particularly useful for angles. To get it to recapitulate the function of mk_angndx, it's as much work as writing the index file by hand. -Justin -- == 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.edu | (410) 706-7441 == -- 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] problem vwith ethanol-water solution
On 10/31/13 2:25 PM, Ehsan Sadeghi wrote: Hi gmx users, I want to solvate nafion molecules in a 3:1 ethanol water solution. I used genbox with -ci option to add ethanol to water when generating the box, but it did not work. Then, first I solvated the ethanol in water, and then added What did not work? In the absence of exact commands and description of the undesirable output, there's little to suggest from such statements. the nafion to the system, but these 3 molecules each sit a part from each other in the box in the pdb file. Any suggestion? http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents -Justin -- == 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.edu | (410) 706-7441 == -- 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] All-bonds vs. H-bonds using CHARMM36
On 10/31/13 2:21 PM, rajat desikan wrote: Hi, In the CHARMM36 paper (Klauda et al., JPCB 2010), only the hydrogen bonds are constrained for the lipid simulations using SHAKE (excerpt from the paper below) Consistent for all of these simulations was the use of a 1 fs time step and constraining of the hydrogen atoms using the SHAKE algorithm. For a membrane-protein system, is constraining all-bonds via LINCS the right option while using CHARMM36? Normally, as the paper states, only bonds involving H are constrained with CHARMM. LINCS is a suitable replacement for SHAKE, though you can use SHAKE in Gromacs if you want. LINCS is generally more robust. There was a mention somewhere (I forgot) that constraining all-bonds probably prevents alkane isomerisations in membranes, which could lower the melting temperature. I intend to simulate a POPC bilayer. Can someone with experience please shed some light on this? Can't comment on this, but I doubt there is any issue if you don't constrain all bonds. P.S.: Klauda et al., has posted their .mdp for POPE in gromacs on lipidbook. Their .mdp constrains h-bonds http://lipidbook.bioch.ox.ac.uk/uploads/package/CHARMM36/48-POPE-wurl/v1/charmm_npt.mdp It is very uncommon that such input files exist without specifically requesting them; if this is exactly what the authors used, I see no reason to deviate from it unless you have a demonstrably superior protocol. -Justin -- == 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.edu | (410) 706-7441 == -- 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 group in index file?
@ Justin, That doesn’t sound very good. I tried it as he suggested using make_ndx, it seems to work, but it’s not reporting the result I want. When I use g_angle using the index i created, I chose the group I want to assess (My compound is very simple in Martini, it’s only represented by 3 atoms) and it reports back to me 1 angle value. However, I wish to assess the angle between atom 1 2, 23 and 13. How should I go about achieving that? Thanks, Xu Huang On Oct 31, 2013, at 4:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/31/13 3:59 PM, Riccardo Concu wrote: Dear Xu, you have to use the make_ndx option if I'm not wrong. The syntax should be make_ndx -f xxx.gro -o index.ndx make_ndx is not particularly useful for angles. To get it to recapitulate the function of mk_angndx, it's as much work as writing the index file by hand. -Justin -- == 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.edu | (410) 706-7441 == -- 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] No group in index file?
On 10/31/13 4:22 PM, Xu Dong Huang wrote: @ Justin, That doesn’t sound very good. I tried it as he suggested using make_ndx, it seems to work, but it’s not reporting the result I want. When I use g_angle using the index i created, I chose the group I want to assess (My compound is very simple in Martini, it’s only represented by 3 atoms) and it reports back to me 1 angle value. However, I wish to assess the angle between atom 1 2, 23 and 13. How should I go about achieving that? If you have 3 atoms/particles, there can be only one angle, by definition. Do you have an [angles] directive in the topology? That's how mk_angndx parses the .tpr file - by creating groups of similar angles based on theta and ktheta. If your model doesn't specify any angle potential, then mk_angndx will bail out and return nothing, though it should probably do that in a more elegant way than producing an empty file. -Justin -- == 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.edu | (410) 706-7441 == -- 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] All-bonds vs. H-bonds using CHARMM36
Thank you, Justin! I did intend to use h-bonds for the CHARMM36 simulations and all-bonds elsewhere (depending on the FF). I just wanted some clarity before I proceeded. On Fri, Nov 1, 2013 at 1:49 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/31/13 2:21 PM, rajat desikan wrote: Hi, In the CHARMM36 paper (Klauda et al., JPCB 2010), only the hydrogen bonds are constrained for the lipid simulations using SHAKE (excerpt from the paper below) Consistent for all of these simulations was the use of a 1 fs time step and constraining of the hydrogen atoms using the SHAKE algorithm. For a membrane-protein system, is constraining all-bonds via LINCS the right option while using CHARMM36? Normally, as the paper states, only bonds involving H are constrained with CHARMM. LINCS is a suitable replacement for SHAKE, though you can use SHAKE in Gromacs if you want. LINCS is generally more robust. There was a mention somewhere (I forgot) that constraining all-bonds probably prevents alkane isomerisations in membranes, which could lower the melting temperature. I intend to simulate a POPC bilayer. Can someone with experience please shed some light on this? Can't comment on this, but I doubt there is any issue if you don't constrain all bonds. P.S.: Klauda et al., has posted their .mdp for POPE in gromacs on lipidbook. Their .mdp constrains h-bonds http://lipidbook.bioch.ox.ac.**uk/uploads/package/CHARMM36/** 48-POPE-wurl/v1/charmm_npt.mdphttp://lipidbook.bioch.ox.ac.uk/uploads/package/CHARMM36/48-POPE-wurl/v1/charmm_npt.mdp It is very uncommon that such input files exist without specifically requesting them; if this is exactly what the authors used, I see no reason to deviate from it unless you have a demonstrably superior protocol. -Justin -- ==** 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 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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 group in index file?
@ Justin, I did not define [angles] in the topology but I do have the angles result from All-atom run using OPLS forcefield. The reason for me not to include it in MARTINI forcefield topology is because I wanted to see if it will produce similar angle result of atom 12, 13 and 23 in martini water since the behavior of particle types I chose for my 3 atoms are well defined by martini at this point. My interest is to find for which force constant K value will the martini model match the all-atom model using OPLS. And you’re right, sorry, I got confused about the angles, there should only be 1. However, even the angle value I received doesn’t match the traditional all-atom result. What will happen if I define the [angles] part with the angles I received from traditional simulation? Because ultimately I am trying to find the k value parameter that will make the 3 particle display an angle similar to traditional run. On Oct 31, 2013, at 4:26 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/31/13 4:22 PM, Xu Dong Huang wrote: @ Justin, That doesn’t sound very good. I tried it as he suggested using make_ndx, it seems to work, but it’s not reporting the result I want. When I use g_angle using the index i created, I chose the group I want to assess (My compound is very simple in Martini, it’s only represented by 3 atoms) and it reports back to me 1 angle value. However, I wish to assess the angle between atom 1 2, 23 and 13. How should I go about achieving that? If you have 3 atoms/particles, there can be only one angle, by definition. Do you have an [angles] directive in the topology? That's how mk_angndx parses the .tpr file - by creating groups of similar angles based on theta and ktheta. If your model doesn't specify any angle potential, then mk_angndx will bail out and return nothing, though it should probably do that in a more elegant way than producing an empty file. -Justin -- == 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.edu | (410) 706-7441 == -- 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] No group in index file?
On 10/31/13 4:44 PM, Xu Dong Huang wrote: @ Justin, I did not define [angles] in the topology but I do have the angles result from All-atom run using OPLS forcefield. The reason for me not to include it in MARTINI forcefield topology is because I wanted to see if it will produce similar angle result of atom 12, 13 and 23 in martini water since the behavior of particle types I chose for my 3 atoms are well defined by martini at this point. My interest is to find for which force constant K value will the martini model match the all-atom model using OPLS. And you’re right, sorry, I got confused about the angles, there should only be 1. However, even the angle value I received doesn’t match the traditional all-atom result. What will happen if I define the [angles] part with the angles I received from traditional simulation? Because ultimately I am trying to find the k value parameter that will make the 3 particle display an angle similar to traditional run. If you define an equilibrium angle for 1-2-3, it will oscillate harmonically around that value, with the distribution determined by the value of k. I suspect that is how you can tune the parameters, by matching the distributions produced in the two simulations rather than a single target value, because with the angle defined in the topology, you're sort of predetermining the outcome. -Justin -- == 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.edu | (410) 706-7441 == -- 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 group in index file?
@ Justin, Excellent advice. Thank you! And for the equilibrium angle, what is the approximate range I can define it to be? Say target is 90 degrees, should I define maybe 130 and let it oscillate? I guess question is how far is too far off? Thanks, On Oct 31, 2013, at 4:48 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/31/13 4:44 PM, Xu Dong Huang wrote: @ Justin, I did not define [angles] in the topology but I do have the angles result from All-atom run using OPLS forcefield. The reason for me not to include it in MARTINI forcefield topology is because I wanted to see if it will produce similar angle result of atom 12, 13 and 23 in martini water since the behavior of particle types I chose for my 3 atoms are well defined by martini at this point. My interest is to find for which force constant K value will the martini model match the all-atom model using OPLS. And you’re right, sorry, I got confused about the angles, there should only be 1. However, even the angle value I received doesn’t match the traditional all-atom result. What will happen if I define the [angles] part with the angles I received from traditional simulation? Because ultimately I am trying to find the k value parameter that will make the 3 particle display an angle similar to traditional run. If you define an equilibrium angle for 1-2-3, it will oscillate harmonically around that value, with the distribution determined by the value of k. I suspect that is how you can tune the parameters, by matching the distributions produced in the two simulations rather than a single target value, because with the angle defined in the topology, you're sort of predetermining the outcome. -Justin -- == 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.edu | (410) 706-7441 == -- 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] No group in index file?
On 10/31/13 5:03 PM, Xu Dong Huang wrote: @ Justin, Excellent advice. Thank you! And for the equilibrium angle, what is the approximate range I can define it to be? Say target is 90 degrees, should I define maybe 130 and let it oscillate? I guess question is how far is too far off? This is what I meant about a predefined outcome. If you set the equilibrium value of the angle at 130 degrees, you're going to get a distribution centered at 130 degrees. The odds of it sampling any configurations at 90 degrees are a function of the force constant, but still would be rare, so this approach makes no sense to me (there is a huge difference between 90 and 130). If the target is 90, set it for 90. Tune the force constant to match the distribution. -Justin Thanks, On Oct 31, 2013, at 4:48 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/31/13 4:44 PM, Xu Dong Huang wrote: @ Justin, I did not define [angles] in the topology but I do have the angles result from All-atom run using OPLS forcefield. The reason for me not to include it in MARTINI forcefield topology is because I wanted to see if it will produce similar angle result of atom 12, 13 and 23 in martini water since the behavior of particle types I chose for my 3 atoms are well defined by martini at this point. My interest is to find for which force constant K value will the martini model match the all-atom model using OPLS. And you’re right, sorry, I got confused about the angles, there should only be 1. However, even the angle value I received doesn’t match the traditional all-atom result. What will happen if I define the [angles] part with the angles I received from traditional simulation? Because ultimately I am trying to find the k value parameter that will make the 3 particle display an angle similar to traditional run. If you define an equilibrium angle for 1-2-3, it will oscillate harmonically around that value, with the distribution determined by the value of k. I suspect that is how you can tune the parameters, by matching the distributions produced in the two simulations rather than a single target value, because with the angle defined in the topology, you're sort of predetermining the outcome. -Justin -- == 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.edu | (410) 706-7441 == -- 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. 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.edu | (410) 706-7441 == -- 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] problem vwith ethanol-water solution
Thanks Justin, Here is the steps that I followed: pdb2gmx -f eth.pdb -o eth.gro -p eth.top pdb2gmx -f ionomer-4.pdb -o ionomer4.gro -p ionomer4.top editconf -f ionomer4.gro -o box.gro -bt dodecahedron -d 0.5 genbox -cp box.gro -cs spc216.gro -ci eth.gro -nmol 1000 -o solvated.gro I got the box with ionomer in ethanol and water solution. However, I only have 400 of eth and 423 water molecule. The box wasn't large enough? What should I do with .top file? I have the .top file for ionomer and .top file for one eth molecule. Kind regards, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, October 31, 2013 1:18:07 PM Subject: Re: [gmx-users] problem vwith ethanol-water solution On 10/31/13 2:25 PM, Ehsan Sadeghi wrote: Hi gmx users, I want to solvate nafion molecules in a 3:1 ethanol water solution. I used genbox with -ci option to add ethanol to water when generating the box, but it did not work. Then, first I solvated the ethanol in water, and then added What did not work? In the absence of exact commands and description of the undesirable output, there's little to suggest from such statements. the nafion to the system, but these 3 molecules each sit a part from each other in the box in the pdb file. Any suggestion? http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents -Justin -- == 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.edu | (410) 706-7441 == -- 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] problem vwith ethanol-water solution
On 10/31/13 7:03 PM, Ehsan Sadeghi wrote: Thanks Justin, Here is the steps that I followed: pdb2gmx -f eth.pdb -o eth.gro -p eth.top pdb2gmx -f ionomer-4.pdb -o ionomer4.gro -p ionomer4.top editconf -f ionomer4.gro -o box.gro -bt dodecahedron -d 0.5 genbox -cp box.gro -cs spc216.gro -ci eth.gro -nmol 1000 -o solvated.gro I got the box with ionomer in ethanol and water solution. However, I only have 400 of eth and 423 water molecule. The box wasn't large enough? Follow the advice at the link I posted before. Trying to add ethanol while simultaneously solvating is a bad idea. If genbox cannot add 1000 ethanol molecules without trying to do anything else, then yes, the box is simply too small. At this point, we can't say because it could simply be that simultaneous solvation might have been competing for available box volume. What should I do with .top file? I have the .top file for ionomer and .top file for one eth molecule. It is simple to covert between .top and .itp and #include them however you see fit. Probably the conceptually easiest methhod is to consider ethanol just like any other solvent (i.e. water) and #include it within the .top for the ionomer, which is just like any other solute. -Justin -- == 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.edu | (410) 706-7441 == -- 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] Hardware for best gromacs performance?
Hi All, I am considering setting up a small cluster to run Gromacs jobs. The aim would be to maximise ns/day/$ for smallish systems of 15-30,000 atoms. Can anybody provide advice/benchmarks/anecdotes about what type of current hardware provides the best performance/price? Would it be something like a dual core xeon system with two (or more?) Titan GPUs? Thanks David --- David Chalmers Senior Lecturer Faculty of Pharmacy and Pharmaceutical Sciences Medicinal Chemistry Monash Institute of Pharmaceutical Sciences Monash University (Parkville campus) 381 Royal Parade, Parkville Victoria 3052, Australia Tel: +61 3 9903 9110 Fax: +61 3 9903 9582 -- 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] probability distribution of bond distance/length
Dear all, I would like to assess the probability distribution of particle bond distance/length over the entire run, specifically I want to collect possibly a histogram representation or even a regular plot. Would using g_bond be the correct way to obtain the probability distribution? Or is there another function that gets probability distribution specifically. Also, if using g_bond, it will give me an average (I suppose), so how can I get a histogram/data series representation? (I do not want to visualize this result using xmgrace) P.S I believe someone earlier suggested a link to the data collection reporting procedure, I tried it and changed the .xvg to a .csv, but the data reported in excel format all belongs to 1 single column, which won’t let me make a plot. Any insight is appreciated it. Xu Huang-- 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] how to get Eigenvectors
Dear GMX Users, I performed an ANM calculation at http://ignmtest.ccbb.pitt.edu/cgi-bin/anm/anm1.cgi It returned me eigenvectors in the following format (where the second and third column represent first and second eigenvector) 1 0.010551 -0.048553 1 -0.022038 -0.042918 1 0.107906 0.045009 2 0.007908 -0.061543 2 -0.002990 -0.054203 2 0.109087 0.062326 . . I tried to convert them into trr file, so that I can use them for analysis and this is where I am stuck. I converted them to PDB and I loose out on the precision of coordinates. ATOM 1 CA LYS A 1 0.011 -0.022 0.108 1.00 10.00 C ATOM 2 CA ILE A 2 0.008 -0.003 0.109 1.00 10.00 C ATOM 3 CA GLU A 3 0.008 0.011 0.077 1.00 10.00 C I added the reference structure (the structure I submitted to the server as frame 1, time 0) to the above PDB file and used g_nmtraj to get the projection. Is there a better way to get the eigenvec.trr. The server also returns Hessian, so can I use this information to get the eigenvec.trr using g_nmeig, but I am not sure how the format of nm.mtx should be. Can someone advice me on how to proceed further. Sincerely, nahren -- 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] GMX manually generate topology for residues
i am a newbie to gromacs, trying to generate a new rtp entry for my residue. Bonds, dihedrals of .rtp file has gb_XX what is gb_XX numbers? how can get informations about that? How to define those velues for my residues? -- 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
