[gmx-users] trajectory analysis
Dear All, I want to ask some questions about trajectory analysis. I have some md simulation output files that includes coordinate, force and velocity information. And these files are huge ( more than 5 GB ) . Could you please recommend a free text editor which works on Linux or Windows to open and editthese huge files? And I will run these files with fortran codes and get again huge output files . In order to do this operation faster and seamlessly what should I do ? Which facilities do I have on pc ? Could you please share your experiences with me ? Thanks for any help. Kind regards.-- 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] trajectory analysis
On 30/05/2012 4:45 PM, oguz gurbulak wrote: Dear All, I want to ask some questions about trajectory analysis. I have some md simulation output files that includes coordinate, force and velocity information. And these files are huge ( more than 5 GB ) . Could you please recommend a free text editor which works on Linux or Windows to open and editthese huge files? And I will run these files with fortran codes and get again huge output files . In order to do this operation faster and seamlessly what should I do ? Which facilities do I have on pc ? Could you please share your experiences with me ? The advice of http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume is applicable to managing these situations. A few minutes of thought can save hours of I/O processing. 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] can Gromacs 4.5 use VDW long range correction? IN the mannual, In this version, GROMACS always uses a cut-off radius for the Lennard-Jones interactions
Hi All, I have to use the long range correction for VDW, in fact i used cut-off=1.4 nm for calculation of surface tension of TIP4P/2005, we can get 65 dyn. The .mdp i used are as follow, I really need to know how to get a surface tension of 69.5 dyn for TIP4P/2005 water model. Becasue my surpervisor is so picky, everything should be perfacet, and i feel really tired by his way. Any comment will be greatly appreciated, The main parameter is coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.4 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 3.8 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 The full .mdp are as follow, ; ; File 'mdout.mdp' was generated ; By user: spoel (291) ; On host: chagall ; At date: Mon Dec 15 13:13:06 2003 ; ; VARIOUS PREPROCESSING OPTIONS title = Yo cpp = /usr/bin/cpp include = define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit = 0 dt = 0.001 nsteps = 40 ; For exact run continuation or redoing part of a run init_step = 0 ; mode for center of mass motion removal comm-mode = Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps = ; LANGEVIN DYNAMICS OPTIONS ; Temperature, friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size ; Max number of iterations in relax_shells niter = 20 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 5000 nstvout = 8000 nstfout = 8000 ; Checkpointing helps you continue after crashes nstcheckpoint = 1000 ; Output frequency for energies to log file and energy file nstlog = 5000 nstenergy = 5000 ; Output frequency and precision for xtc file nstxtcout = 500 xtc-precision = 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist = 1.4 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.4 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 3.8 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = v-rescale ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t = 0.1 ref_t = 300 ; Pressure coupling Pcoupl = no Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p = 1 compressibility = 4.5e-5 ref_p = 1.0 ; Random seed for Andersen thermostat andersen_seed = 815131 ; SIMULATED ANNEALING ; Type of annealing for each temperature group (no/single/periodic) annealing = no ; Number of time points to use for specifying annealing in each group annealing_npoints = ; List of times at the annealing points for each group annealing_time = ; Temp. at each annealing point, for each group. annealing_temp = ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 300 gen_seed = 1993 ; OPTIONS FOR BONDS constraints = none ; Type of constraint algorithm constraint-algorithm = Lincs ; Do not constrain the start configuration unconstrained-start = no ; Use successive
Re: [gmx-users] can Gromacs 4.5 use VDW long range correction? IN the mannual, In this version, GROMACS always uses a cut-off radius for the Lennard-Jones interactions
On 30/05/2012 5:33 PM, MD wrote: Hi All, I have to use the long range correction for VDW, in fact i used cut-off=1.4 nm for calculation of surface tension of TIP4P/2005, we can get 65 dyn. The .mdp i used are as follow, I really need to know how to get a surface tension of 69.5 dyn for TIP4P/2005 water model. By finding the method that was used then and attempting to replicate it? Becasue my surpervisor is so picky, everything should be perfacet, and i feel really tired by his way. Any comment will be greatly appreciated, A certain degree of pickiness is essential. You're apparently trying to replicate a result by making some arbitrary choices. Don't. This .mdp file generates velocities, thus did not start in an equilibrium ensemble. However you measured your surface tension needs to exclude the equilibration time. Mark The main parameter is coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.4 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 3.8 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 The full .mdp are as follow, ; ; File 'mdout.mdp' was generated ; By user: spoel (291) ; On host: chagall ; At date: Mon Dec 15 13:13:06 2003 ; ; VARIOUS PREPROCESSING OPTIONS title = Yo cpp = /usr/bin/cpp include = define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit = 0 dt = 0.001 nsteps = 40 ; For exact run continuation or redoing part of a run init_step = 0 ; mode for center of mass motion removal comm-mode = Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps = ; LANGEVIN DYNAMICS OPTIONS ; Temperature, friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size ; Max number of iterations in relax_shells niter = 20 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 5000 nstvout = 8000 nstfout = 8000 ; Checkpointing helps you continue after crashes nstcheckpoint = 1000 ; Output frequency for energies to log file and energy file nstlog = 5000 nstenergy = 5000 ; Output frequency and precision for xtc file nstxtcout = 500 xtc-precision = 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist = 1.4 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.4 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 3.8 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = v-rescale ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t = 0.1 ref_t = 300 ; Pressure coupling Pcoupl = no Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p = 1 compressibility = 4.5e-5 ref_p = 1.0 ; Random seed for Andersen thermostat andersen_seed = 815131 ; SIMULATED ANNEALING ; Type of annealing for each temperature group (no/single/periodic) annealing = no ; Number of time points to use for specifying annealing in each group annealing_npoints = ; List of times at the annealing
[gmx-users] xmgrace-plotting of g_sas output (averages+standarddeviation)
Hello, I am currently analyzing a bunch of trajectories and one thing I am doing is to use g_sas to generate the average and standard deviation per residue. The resulting xvg file should be formatted for use with xmgrace but I do not seem to be able to get the standard deviation in the graph. I tried searching for some hints and also looked through xmgrace's manual but there was nothing about file format where the second column is the standardeviation and how to show that in the graph. Can anyone of you maybe point me in the right direction on how to plot the averages plus the corresponding standard deviation? Best Marc -- 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] Fw:Re:gmx-users Digest, Vol 97, Issue 218
Yes, i try to get a surface tension of 69 dyn, but i can only get 65 at present. Yes, i tried some arbitrary choices. I do not know what is the correct .mdp for me to get a surface tension of 69. May be for this version, it does not include this function Thanks for your kind message. But i still does not how to figure it out. At 2012-05-30 15:43:36,gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. can Gromacs 4.5 use VDW long range correction? IN the mannual, In this version, GROMACS always uses a cut-off radius for the Lennard-Jones interactions (MD) 2. Re: can Gromacs 4.5 use VDW long range correction? INthe mannual, In this version,GROMACS always uses a cut-off radius for the Lennard-Jones interactions (Mark Abraham) -- Message: 1 Date: Wed, 30 May 2012 15:33:53 +0800 (CST) From: MD ptf1...@163.com Subject: [gmx-users] can Gromacs 4.5 use VDW long range correction? IN the mannual, In this version, GROMACS always uses a cut-off radius for the Lennard-Jones interactions To: gmx-users@gromacs.org Message-ID: 1dc9ba2d.c95b.1379caa467e.coremail.ptf1...@163.com Content-Type: text/plain; charset=gbk Hi All, I have to use the long range correction for VDW, in fact i used cut-off=1.4 nm for calculation of surface tension of TIP4P/2005, we can get 65 dyn. The .mdp i used are as follow, I really need to know how to get a surface tension of 69.5 dyn for TIP4P/2005 water model. Becasue my surpervisor is so picky, everything should be perfacet, and i feel really tired by his way. Any comment will be greatly appreciated, The main parameter is coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.4 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 3.8 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 Message: 2 Date: Wed, 30 May 2012 17:42:57 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] can Gromacs 4.5 use VDW long range correction? IN the mannual, In this version, GROMACS always uses a cut-off radius for the Lennard-Jones interactions To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4fc5cf81.7000...@anu.edu.au Content-Type: text/plain; charset=iso-8859-1 On 30/05/2012 5:33 PM, MD wrote: Hi All, I have to use the long range correction for VDW, in fact i used cut-off=1.4 nm for calculation of surface tension of TIP4P/2005, we can get 65 dyn. The .mdp i used are as follow, I really need to know how to get a surface tension of 69.5 dyn for TIP4P/2005 water model. By finding the method that was used then and attempting to replicate it? Becasue my surpervisor is so picky, everything should be perfacet, and i feel really tired by his way. Any comment will be greatly appreciated, A certain degree of pickiness is essential. You're apparently trying to replicate a result by making some arbitrary choices. Don't. This .mdp file generates velocities, thus did not start in an equilibrium ensemble. However you measured your surface tension needs to exclude the equilibration time. 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
Re: [gmx-users] Fw:Re:gmx-users Digest, Vol 97, Issue 218
On 30/05/2012 7:24 PM, MD wrote: Yes, i try to get a surface tension of 69 dyn, but i can only get 65 at present. Yes, i tried some arbitrary choices. I do not know what is the correct .mdp for me to get a surface tension of 69. May be for this version, it does not include this function Making arbitrary choices is a bad approach. When that fails, assuming that there's a limitation in the software that you are using is even worse. Someone used a specific method to get the number someone claims you should be getting. You need to go and find out what that that method was. Yes, this is more work than assuming that GROMACS can't reproduce the method. Welcome to the jungle :-) 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] Lipid A Topology
Hello everyone, As a follow up to my message last week regarding the addition of phospholipid (PC, PE, PG and Cardiolipin) topologies to the Lipidbook website, I am happy to announce that we have also added parameters for lipid A from E. coli. Lipid A is the lipidic component of lipopolysaccharide, which is found in the outer membranes of Gram-negative bacteria. If you use these parameters please read and cite the following work: Electroporation of the E. coli and S. aureus Membranes: Molecular Dynamics Simulations of Complex Bacterial Membranes Thomas J. Piggot, Daniel A. Holdbrook, and Syma Khalid J. Phys. Chem. B 2011, 115 (45), pp 13381–13388 http://pubs.acs.org/doi/abs/10.1021/jp207013v To access the parameters you can use the following link: http://lipidbook.bioch.ox.ac.uk/package/show/id/62.html In addition, these parameters will soon be made available on our group website (http://www.personal.soton.ac.uk/sk2x07/index.php), along with a structure file for this molecule. Cheers Tom Piggot -- Dr Thomas Piggot University of Southampton, UK. -- 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] can Gromacs 4.5 use VDW long range correction? IN the mannual, In this version, GROMACS always uses a cut-off radius for the Lennard-Jones interactions
Hi, I do not know, how TIP4P/2005 has been parametrized, but the VdW cutoff you are using is quite large. Did the authors of TIP4P/2005 really applied this large cutoff ? This is very important, because the force field is always parameterised in respect to certain parameters and vdW is an essential one. Increasing or decreasing the value suggested by the authors can yield serious artefacts. /Flo On Wed, 2012-05-30 at 15:33 +0800, MD wrote: Hi All, I have to use the long range correction for VDW, in fact i used cut-off=1.4 nm for calculation of surface tension of TIP4P/2005, we can get 65 dyn. The .mdp i used are as follow, I really need to know how to get a surface tension of 69.5 dyn for TIP4P/2005 water model. Becasue my surpervisor is so picky, everything should be perfacet, and i feel really tired by his way. Any comment will be greatly appreciated, The main parameter is coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.4 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 3.8 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 The full .mdp are as follow, ; ; File 'mdout.mdp' was generated ; By user: spoel (291) ; On host: chagall ; At date: Mon Dec 15 13:13:06 2003 ; ; VARIOUS PREPROCESSING OPTIONS title = Yo cpp = /usr/bin/cpp include = define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit = 0 dt = 0.001 nsteps = 40 ; For exact run continuation or redoing part of a run init_step = 0 ; mode for center of mass motion removal comm-mode = Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps = ; LANGEVIN DYNAMICS OPTIONS ; Temperature, friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size ; Max number of iterations in relax_shells niter = 20 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 5000 nstvout = 8000 nstfout = 8000 ; Checkpointing helps you continue after crashes nstcheckpoint = 1000 ; Output frequency for energies to log file and energy file nstlog = 5000 nstenergy = 5000 ; Output frequency and precision for xtc file nstxtcout = 500 xtc-precision = 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist = 1.4 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.4 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 3.8 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = v-rescale ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t = 0.1 ref_t = 300 ; Pressure coupling Pcoupl = no Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar)
Re: [gmx-users] xmgrace-plotting of g_sas output (averages+standarddeviation)
On 5/30/12 4:58 AM, Marc Hömberger wrote: Hello, I am currently analyzing a bunch of trajectories and one thing I am doing is to use g_sas to generate the average and standard deviation per residue. The resulting xvg file should be formatted for use with xmgrace but I do not seem to be able to get the standard deviation in the graph. I tried searching for some hints and also looked through xmgrace's manual but there was nothing about file format where the second column is the standardeviation and how to show that in the graph. Can anyone of you maybe point me in the right direction on how to plot the averages plus the corresponding standard deviation? In the window for importing data, choose XYDY from the Set type dropdown menu. -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] Regarding g_wham options
Hi all, I want to set the lowest point in my curve as zero instead of negative number. Can anyone tell me which option to use to do that? -- Regards, Nitin Agrawal, Master's Student (Bioinformatics) University of Turku,Finland B.Tech (Biotechnology) National Institute of Technology,Durgapur,India Blog:http://notjustanyotherblog.blogspot.com/ attachment: profile_all.jpg-- 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] Regarding g_wham options
On 5/30/12 6:29 AM, Nitin Agrawal wrote: Hi all, I want to set the lowest point in my curve as zero instead of negative number. Can anyone tell me which option to use to do that? Set the desired value with -zprof0. -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
Re: [gmx-users] Regarding g_wham options
Thank you On Wed, May 30, 2012 at 1:39 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 5/30/12 6:29 AM, Nitin Agrawal wrote: Hi all, I want to set the lowest point in my curve as zero instead of negative number. Can anyone tell me which option to use to do that? Set the desired value with -zprof0. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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 -- Regards, Nitin Agrawal, Master's Student (Bioinformatics) University of Turku,Finland B.Tech (Biotechnology) National Institute of Technology,Durgapur,India Blog:http://notjustanyotherblog.blogspot.com/ -- 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] angling bond at at one of the terminal ends
hi, recently while working on gromacs i came across this error There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. i tried to edit .tdb file by giving the terminal entries but its not working.. plz help me out regards, ram -- View this message in context: http://gromacs.5086.n6.nabble.com/angling-bond-at-at-one-of-the-terminal-ends-tp4997894.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] angling bond at at one of the terminal ends
On 30/05/2012 9:30 PM, ramaraju801 wrote: hi, recently while working on gromacs i came across this error There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. i tried to edit .tdb file by giving the terminal entries but its not working.. plz help me out You need to describe what you are trying to do and how you attempted to do it in a lot more detail before anybody can help you. 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] Re: Possible bug: energy changes with the number of nodes for energy minimization
Hi Justin, Thanks for getting back and posting the links. On 5/29/12 6:22 AM, Stephen Cox wrote: Hi, I'm running a number of energy minimizations on a clathrate supercell and I get quite significantly different values for the total energy depending on the number of mpi processes / number of threads I use. More specifically, some numbers I get are: #cores energy 1-2.41936409202696e+04 2-2.43726425776809e+04 3-2.45516442350804e+04 4-2.47003944216983e+04 #threadsenergy 1-2.41936409202696e+04 2-2.43726425776792e+04 3-2.45516442350804e+04 4-2.47306458924815e+04 I'd expect some numerical noise, but these differences seem to0 large for that. The difference is only 2%, which by MD standards, is quite good, I'd say ;) Consider the discussion here: I agree for MD this wouldn't be too bad, but I'd expect energy minimization to get very close to the same local minimum from a given starting configuration. The thing is I want to compute a binding curve for my clathrate and compare to DFT values for the binding energy (amongst other things), and the difference in energy between different number of cores is rather significant for this purpose. Furthermore, if I only calculate the energy for nsteps = 0 (i.e. a single point energy for identical structures) I get the same trend as above (both mpi/openmp with domain/particle decomposition). Surely there shouldn't be such a large difference in energy for a single point calculation? http://www.gromacs.org/Documentation/Terminology/Reproducibility To an extent, the information here may also be relevant: http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation Before submitting a bug report, I'd like to check: a) if someone has seen something similar; Sure. Energies can be different due to a whole host of factors (discussed above), and MPI only complicates matters. b) should I just trust the serial version? Maybe, but I don't know that there's evidence to say that any of the above tests are more or less accurate than the others. What happens if you run with mdrun -reprod on all your tests? Running with -reprod produces the same trend as above. If it was numerical noise, I would have thought that the numbers would fluctuate around some average value, not follow a definite trend where the energy decreases with the number of cores/threads... c) have I simply done something stupid (grompp.mdp appended below); Nope, looks fine. -Justin Thanks again for getting back to me. -- 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] xmgrace-plotting of g_sas output (averages+standarddeviation)
Hi, when I try the mentioned method for the GROMACs output (xvg file, supposedly formatted for use with xmgrace) I am unable to print the standarddeviation. I f I select the XYDY method it just ignores it and plots again an XY graph. What I then did: I stripped the file so that only residue number (column 1), average (column 2) and the standarddeviation (column 3) are in the file (each comma seperated by a single space). When i open that in xmgrace and I select the XYDY set it is displayed correctly. However, this means I have to strip each file. Is there any way I can circumvent stripping every single file? Best Marc On Wed, May 30, 2012 at 6:22 AM, Justin A. Lemkul jalem...@vt.edu wrote: On 5/30/12 4:58 AM, Marc Hömberger wrote: Hello, I am currently analyzing a bunch of trajectories and one thing I am doing is to use g_sas to generate the average and standard deviation per residue. The resulting xvg file should be formatted for use with xmgrace but I do not seem to be able to get the standard deviation in the graph. I tried searching for some hints and also looked through xmgrace's manual but there was nothing about file format where the second column is the standardeviation and how to show that in the graph. Can anyone of you maybe point me in the right direction on how to plot the averages plus the corresponding standard deviation? In the window for importing data, choose XYDY from the Set type dropdown menu. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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 -- 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: Possible bug: energy changes with the number of nodes for energy minimization
On 30/05/2012 9:42 PM, Stephen Cox wrote: Hi Justin, Thanks for getting back and posting the links. On 5/29/12 6:22 AM, Stephen Cox wrote: Hi, I'm running a number of energy minimizations on a clathrate supercell and I get quite significantly different values for the total energy depending on the number of mpi processes / number of threads I use. More specifically, some numbers I get are: #cores energy 1-2.41936409202696e+04 2-2.43726425776809e+04 3-2.45516442350804e+04 4-2.47003944216983e+04 #threadsenergy 1-2.41936409202696e+04 2-2.43726425776792e+04 3-2.45516442350804e+04 4-2.47306458924815e+04 I'd expect some numerical noise, but these differences seem to0 large for that. The difference is only 2%, which by MD standards, is quite good, I'd say ;) Consider the discussion here: I agree for MD this wouldn't be too bad, but I'd expect energy minimization to get very close to the same local minimum from a given starting configuration. The thing is I want to compute a binding curve for my clathrate and compare to DFT values for the binding energy (amongst other things), and the difference in energy between different number of cores is rather significant for this purpose. Given the usual roughness of the PE surface to which you are minimizing, some variation in end point is expected. Furthermore, if I only calculate the energy for nsteps = 0 (i.e. a single point energy for identical structures) I get the same trend as above (both mpi/openmp with domain/particle decomposition). Surely there shouldn't be such a large difference in energy for a single point calculation? nsteps = 0 is not strictly a single-point energy, since the constraints act before EM step 0. mdrun -s -rerun will give a single point. This probably won't change your observations. You should also be sure you're making observations with the latest release (4.5.5). If you can continue to observe this trend for more processors (overallocating?), then you may have evidence of a problem - but a full system description and an .mdp file will be in order also. Mark http://www.gromacs.org/Documentation/Terminology/Reproducibility To an extent, the information here may also be relevant: http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation Before submitting a bug report, I'd like to check: a) if someone has seen something similar; Sure. Energies can be different due to a whole host of factors (discussed above), and MPI only complicates matters. b) should I just trust the serial version? Maybe, but I don't know that there's evidence to say that any of the above tests are more or less accurate than the others. What happens if you run with mdrun -reprod on all your tests? Running with -reprod produces the same trend as above. If it was numerical noise, I would have thought that the numbers would fluctuate around some average value, not follow a definite trend where the energy decreases with the number of cores/threads... c) have I simply done something stupid (grompp.mdp appended below); Nope, looks fine. -Justin Thanks again for getting back to me. -- 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: Possible bug: energy changes with the number of nodes for energy minimization
On 5/30/12 7:42 AM, Stephen Cox wrote: Hi Justin, Thanks for getting back and posting the links. On 5/29/12 6:22 AM, Stephen Cox wrote: Hi, I'm running a number of energy minimizations on a clathrate supercell and I get quite significantly different values for the total energy depending on the number of mpi processes / number of threads I use. More specifically, some numbers I get are: #cores energy 1-2.41936409202696e+04 2-2.43726425776809e+04 3-2.45516442350804e+04 4-2.47003944216983e+04 #threadsenergy 1-2.41936409202696e+04 2-2.43726425776792e+04 3-2.45516442350804e+04 4-2.47306458924815e+04 I'd expect some numerical noise, but these differences seem to0 large for that. The difference is only 2%, which by MD standards, is quite good, I'd say ;) Consider the discussion here: I agree for MD this wouldn't be too bad, but I'd expect energy minimization to get very close to the same local minimum from a given starting configuration. The thing is I want to compute a binding curve for my clathrate and compare to DFT values for the binding energy (amongst other things), and the difference in energy between different number of cores is rather significant for this purpose. I think the real issue comes down to how you're going to calculate binding energy. I would still expect that with sufficient MD sampling, the differences should be small or statistically insignificant given the nature of MD calculations. EM will likely be very sensitive to the nature of how it is run (MPI vs. serial, etc) since even the tiny rounding errors and other factors described below will cause changes in how the EM algorithm proceeds. For most purposes, such differences are irrelevant as EM is only a preparatory step for more intense calculations. Furthermore, if I only calculate the energy for nsteps = 0 (i.e. a single point energy for identical structures) I get the same trend as above (both mpi/openmp with domain/particle decomposition). Surely there shouldn't be such a large difference in energy for a single point calculation? That depends. Are you using the same .mdp file, just setting nsteps = 0? If so, that's not a good test. EM algorithms will make a change at step 0, the magnitude of which will again reflect the differences you're seeing. If you use the md integrator with a zero-step evaluation, that's a better test. -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
Re: [gmx-users] Regarding g_wham options
When I am using the command -zprof0. it is not giving the desired result. I am using it as g_wham -b 5000 -zprof0 -6.0 -it tpr_files.dat -if pullf_files.dat -o profile_new1.xvg -hist histo_new1.xvg -unit kCal but the lowest point in the graph is still -6.0 in the y axis and not set to 0.0 Am i using the parameters wrong? On Wed, May 30, 2012 at 1:42 PM, Nitin Agrawal nitinyugalagra...@gmail.comwrote: Thank you On Wed, May 30, 2012 at 1:39 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 5/30/12 6:29 AM, Nitin Agrawal wrote: Hi all, I want to set the lowest point in my curve as zero instead of negative number. Can anyone tell me which option to use to do that? Set the desired value with -zprof0. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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 -- Regards, Nitin Agrawal, Master's Student (Bioinformatics) University of Turku,Finland B.Tech (Biotechnology) National Institute of Technology,Durgapur,India Blog:http://notjustanyotherblog.blogspot.com/ -- Regards, Nitin Agrawal, Master's Student (Bioinformatics) University of Turku,Finland B.Tech (Biotechnology) National Institute of Technology,Durgapur,India Blog:http://notjustanyotherblog.blogspot.com/ -- 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] Regarding g_wham options
On 5/30/12 8:18 AM, Nitin Agrawal wrote: When I am using the command -zprof0. it is not giving the desired result. I am using it as g_wham -b 5000 -zprof0 -6.0 -it tpr_files.dat -if pullf_files.dat -o profile_new1.xvg -hist histo_new1.xvg -unit kCal but the lowest point in the graph is still -6.0 in the y axis and not set to 0.0 Am i using the parameters wrong? From g_wham -h: -zprof0 real 0 Define profile to 0.0 at this position (with -log) The value provided should be the point along the x-axis (the reaction coordinate) where you want the value of the PMF (on the y-axis) to be zero. Your original plot only contained values between about -2 and 2, so specifying -6 is not valid. -Justin On Wed, May 30, 2012 at 1:42 PM, Nitin Agrawal nitinyugalagra...@gmail.com mailto:nitinyugalagra...@gmail.com wrote: Thank you On Wed, May 30, 2012 at 1:39 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 5/30/12 6:29 AM, Nitin Agrawal wrote: Hi all, I want to set the lowest point in my curve as zero instead of negative number. Can anyone tell me which option to use to do that? Set the desired value with -zprof0. -Justin -- ==__== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Regards, Nitin Agrawal, Master's Student (Bioinformatics) University of Turku,Finland B.Tech (Biotechnology) National Institute of Technology,Durgapur,India Blog:http://notjustanyotherblog.blogspot.com/ -- Regards, Nitin Agrawal, Master's Student (Bioinformatics) University of Turku,Finland B.Tech (Biotechnology) National Institute of Technology,Durgapur,India Blog:http://notjustanyotherblog.blogspot.com/ -- 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
Re: [gmx-users] Regarding g_wham options
How can I define the value at y axis then? Is there any way to bring the y-axis value down to 0? On Wed, May 30, 2012 at 3:24 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 5/30/12 8:18 AM, Nitin Agrawal wrote: When I am using the command -zprof0. it is not giving the desired result. I am using it as g_wham -b 5000 -zprof0 -6.0 -it tpr_files.dat -if pullf_files.dat -o profile_new1.xvg -hist histo_new1.xvg -unit kCal but the lowest point in the graph is still -6.0 in the y axis and not set to 0.0 Am i using the parameters wrong? From g_wham -h: -zprof0 real 0 Define profile to 0.0 at this position (with -log) The value provided should be the point along the x-axis (the reaction coordinate) where you want the value of the PMF (on the y-axis) to be zero. Your original plot only contained values between about -2 and 2, so specifying -6 is not valid. -Justin On Wed, May 30, 2012 at 1:42 PM, Nitin Agrawal nitinyugalagra...@gmail.com mailto:nitinyugalagrawal@**gmail.com nitinyugalagra...@gmail.com wrote: Thank you On Wed, May 30, 2012 at 1:39 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 5/30/12 6:29 AM, Nitin Agrawal wrote: Hi all, I want to set the lowest point in my curve as zero instead of negative number. Can anyone tell me which option to use to do that? Set the desired value with -zprof0. -Justin -- ==**__== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing list gmx-users@gromacs.org mailto: gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users 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/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://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 mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Regards, Nitin Agrawal, Master's Student (Bioinformatics) University of Turku,Finland B.Tech (Biotechnology) National Institute of Technology,Durgapur,India Blog:http://**notjustanyotherblog.blogspot.**com/http://notjustanyotherblog.blogspot.com/ -- Regards, Nitin Agrawal, Master's Student (Bioinformatics) University of Turku,Finland B.Tech (Biotechnology) National Institute of Technology,Durgapur,India Blog:http://**notjustanyotherblog.blogspot.**com/http://notjustanyotherblog.blogspot.com/ -- ==**== 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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 -- Regards, Nitin Agrawal, Master's Student (Bioinformatics) University of Turku,Finland B.Tech (Biotechnology) National Institute of Technology,Durgapur,India Blog:http://notjustanyotherblog.blogspot.com/ -- 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
Re: [gmx-users] Regarding g_wham options
On 5/30/12 8:57 AM, Nitin Agrawal wrote: How can I define the value at y axis then? Is there any way to bring the y-axis value down to 0? You want the energy minimum to be equal to zero, correct? This is nothing more than a reference point, so the value passed to -zprof0 is the coordinate value (x-axis) at which the energy minimum occurs. Setting a proper value will shift the curve such that the energy minimum is at zero. -Justin On Wed, May 30, 2012 at 3:24 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 5/30/12 8:18 AM, Nitin Agrawal wrote: When I am using the command -zprof0. it is not giving the desired result. I am using it as g_wham -b 5000 -zprof0 -6.0 -it tpr_files.dat -if pullf_files.dat -o profile_new1.xvg -hist histo_new1.xvg -unit kCal but the lowest point in the graph is still -6.0 in the y axis and not set to 0.0 Am i using the parameters wrong? From g_wham -h: -zprof0 real 0 Define profile to 0.0 at this position (with -log) The value provided should be the point along the x-axis (the reaction coordinate) where you want the value of the PMF (on the y-axis) to be zero. Your original plot only contained values between about -2 and 2, so specifying -6 is not valid. -Justin On Wed, May 30, 2012 at 1:42 PM, Nitin Agrawal nitinyugalagra...@gmail.com mailto:nitinyugalagra...@gmail.com mailto:nitinyugalagrawal@__gmail.com mailto:nitinyugalagra...@gmail.com wrote: Thank you On Wed, May 30, 2012 at 1:39 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 5/30/12 6:29 AM, Nitin Agrawal wrote: Hi all, I want to set the lowest point in my curve as zero instead of negative number. Can anyone tell me which option to use to do that? Set the desired value with -zprof0. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/__Support/Mailing_Lists/Search 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 mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-request@__gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Regards, Nitin Agrawal, Master's Student (Bioinformatics) University of Turku,Finland B.Tech (Biotechnology) National Institute of Technology,Durgapur,India Blog:http://__notjustanyotherblog.blogspot.__com/ http://notjustanyotherblog.blogspot.com/ -- Regards, Nitin Agrawal, Master's Student (Bioinformatics) University of Turku,Finland B.Tech (Biotechnology) National Institute of Technology,Durgapur,India Blog:http://__notjustanyotherblog.blogspot.__com/ http://notjustanyotherblog.blogspot.com/ -- ==__== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080
Re: [gmx-users] xmgrace-plotting of g_sas output (averages+standarddeviation)
On 5/30/12 7:47 AM, Marc Hömberger wrote: Hi, when I try the mentioned method for the GROMACs output (xvg file, supposedly formatted for use with xmgrace) I am unable to print the standarddeviation. I f I select the XYDY method it just ignores it and plots again an XY graph. What I then did: I stripped the file so that only residue number (column 1), average (column 2) and the standarddeviation (column 3) are in the file (each comma seperated by a single space). When i open that in xmgrace and I select the XYDY set it is displayed correctly. However, this means I have to strip each file. Is there any way I can circumvent stripping every single file? Remove or comment out the @TYPE xy line. -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
Re: [gmx-users] Regarding g_wham options
On 5/30/12 9:17 AM, Nitin Agrawal wrote: I got this by using the command : g_wham -b 5000 -zprof0 -2.0 -it tpr_files.dat -if pullf_files.dat -o profile_new1.xvg -hist histo_new1.xvg -unit kCal is their any way to shift the 0 in the y axis so it corresponds to -2 in the x-axis. It is just to make the graph look neater and the calculations to become easier That's precisely what your command is doing. The data in the PMF curve are dependent upon how the umbrella sampling calculations were conducted. There is no way to manipulate the positions of values along the curve, nor should you want to. The -zprof0 option simply allows you to choose a convenient reference point, since free energy is calculated as the difference between two states. Any further manipulation would be spurious. -Justin On Wed, May 30, 2012 at 4:08 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 5/30/12 8:57 AM, Nitin Agrawal wrote: How can I define the value at y axis then? Is there any way to bring the y-axis value down to 0? You want the energy minimum to be equal to zero, correct? This is nothing more than a reference point, so the value passed to -zprof0 is the coordinate value (x-axis) at which the energy minimum occurs. Setting a proper value will shift the curve such that the energy minimum is at zero. -Justin On Wed, May 30, 2012 at 3:24 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 5/30/12 8:18 AM, Nitin Agrawal wrote: When I am using the command -zprof0. it is not giving the desired result. I am using it as g_wham -b 5000 -zprof0 -6.0 -it tpr_files.dat -if pullf_files.dat -o profile_new1.xvg -hist histo_new1.xvg -unit kCal but the lowest point in the graph is still -6.0 in the y axis and not set to 0.0 Am i using the parameters wrong? From g_wham -h: -zprof0 real 0 Define profile to 0.0 at this position (with -log) The value provided should be the point along the x-axis (the reaction coordinate) where you want the value of the PMF (on the y-axis) to be zero. Your original plot only contained values between about -2 and 2, so specifying -6 is not valid. -Justin On Wed, May 30, 2012 at 1:42 PM, Nitin Agrawal nitinyugalagra...@gmail.com mailto:nitinyugalagra...@gmail.com mailto:nitinyugalagrawal@__gmail.com mailto:nitinyugalagra...@gmail.com mailto:nitinyugalagrawal@ mailto:nitinyugalagrawal@__gm__ail.com http://gmail.com mailto:nitinyugalagrawal@__gmail.com mailto:nitinyugalagra...@gmail.com wrote: Thank you On Wed, May 30, 2012 at 1:39 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 5/30/12 6:29 AM, Nitin Agrawal wrote: Hi all, I want to set the lowest point in my curve as zero instead of negative number. Can anyone tell me which option to use to do that? Set the desired value with -zprof0. -Justin -- ==__== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/__justin http://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org__
Re: [gmx-users] Regarding g_wham options
Ok, Thank you once again. On Wed, May 30, 2012 at 4:20 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 5/30/12 9:17 AM, Nitin Agrawal wrote: I got this by using the command : g_wham -b 5000 -zprof0 -2.0 -it tpr_files.dat -if pullf_files.dat -o profile_new1.xvg -hist histo_new1.xvg -unit kCal is their any way to shift the 0 in the y axis so it corresponds to -2 in the x-axis. It is just to make the graph look neater and the calculations to become easier That's precisely what your command is doing. The data in the PMF curve are dependent upon how the umbrella sampling calculations were conducted. There is no way to manipulate the positions of values along the curve, nor should you want to. The -zprof0 option simply allows you to choose a convenient reference point, since free energy is calculated as the difference between two states. Any further manipulation would be spurious. -Justin On Wed, May 30, 2012 at 4:08 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 5/30/12 8:57 AM, Nitin Agrawal wrote: How can I define the value at y axis then? Is there any way to bring the y-axis value down to 0? You want the energy minimum to be equal to zero, correct? This is nothing more than a reference point, so the value passed to -zprof0 is the coordinate value (x-axis) at which the energy minimum occurs. Setting a proper value will shift the curve such that the energy minimum is at zero. -Justin On Wed, May 30, 2012 at 3:24 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 5/30/12 8:18 AM, Nitin Agrawal wrote: When I am using the command -zprof0. it is not giving the desired result. I am using it as g_wham -b 5000 -zprof0 -6.0 -it tpr_files.dat -if pullf_files.dat -o profile_new1.xvg -hist histo_new1.xvg -unit kCal but the lowest point in the graph is still -6.0 in the y axis and not set to 0.0 Am i using the parameters wrong? From g_wham -h: -zprof0 real 0 Define profile to 0.0 at this position (with -log) The value provided should be the point along the x-axis (the reaction coordinate) where you want the value of the PMF (on the y-axis) to be zero. Your original plot only contained values between about -2 and 2, so specifying -6 is not valid. -Justin On Wed, May 30, 2012 at 1:42 PM, Nitin Agrawal nitinyugalagra...@gmail.com mailto:nitinyugalagrawal@**gmail.comnitinyugalagra...@gmail.com mailto:nitinyugalagrawal@__gm**ail.com http://gmail.commailto: nitinyugalagrawal@**gmail.com nitinyugalagra...@gmail.com mailto:nitinyugalagrawal@ mailto:nitinyugalagrawal@__g** m__ail.com http://gm__ail.com http://gmail.com mailto:nitinyugalagrawal@__gm**ail.com http://gmail.com mailto:nitinyugalagrawal@**gmail.comnitinyugalagra...@gmail.com wrote: Thank you On Wed, May 30, 2012 at 1:39 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto: jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 5/30/12 6:29 AM, Nitin Agrawal wrote: Hi all, I want to set the lowest point in my curve as zero instead of negative number. Can anyone tell me which option to use to do that? Set the desired value with -zprof0. -Justin -- ==**__== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/**justinhttp://vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/**justinhttp://vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/**__justinhttp://vt.edu/Pages/Personal/__justin http://vt.edu/Pages/Personal/**justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem._**___vt.edu/Pages/Personal/**justinhttp://vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/**justinhttp://vt.edu/Pages/Personal/justin
Re: [gmx-users] Possible bug: energy changes with the number of nodes for energy minimization
On Tue, May 29, 2012 at 1:22 PM, Stephen Cox stephen.cox...@ucl.ac.uk wrote: I'm running a number of energy minimizations on a clathrate supercell and I get quite significantly different values for the total energy depending on the number of mpi processes / number of threads I use. You are probably seeing this: http://redmine.gromacs.org/issues/901 - Teemu -- 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] OPLS specific problem in gromacs 4.5.4
After creating a box using editconf and then solvating using genbox, I try to add ions and get the infamous number of coordinates in .gro does not match number of coordinates in topology error. What's strange is that it only seems to happen when I am using the OPLS force field. I can type the exact same sequence of commands using the CHARMM27 force field and I don't get the error (unfortunately I want to use OPLS). Has anyone else encountered this? BTW, I tried dos2unix-ing my .mdp file before using grompp, but that didn't help. Any suggestions? Thanks. Patrick L. Wintrode School of Pharmacy University of Maryland -- 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] OPLS specific problem in gromacs 4.5.4
On 5/30/12 11:32 AM, patrick wintrode wrote: After creating a box using editconf and then solvating using genbox, I try to add ions and get the infamous number of coordinates in .gro does not match number of coordinates in topology error. What's strange is that it only seems to happen when I am using the OPLS force field. I can type the exact same sequence of commands using the CHARMM27 force field and I don't get the error (unfortunately I want to use OPLS). Has anyone else encountered this? BTW, I tried dos2unix-ing my .mdp file before using grompp, but that didn't help. Any suggestions? Can you verify that the contents of the coordinate and topology files indeed should match? For instance, have you manually inspected them and counted water molecules, etc to guarantee they are the same? If you are using different force fields, have you verified that you are using the right files that match the given force field? Does the water model you solvated with match the coordinate file? TIP3P is suggested for CHARMM, but TIP4P is suggested for OPLS, so the same sequence of commands might give different outcomes. Have you tried your workflow with CHARMM and OPLS via a script, so that you know that what you typed in each case was exactly the same? -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] Re: Possible bug: energy changes with the number of nodes for energy minimization
Hi Justin and Mark, Thanks once again for getting back. I've found the problem - it's actually a known bug already: http://redmine.gromacs.org/issues/901 The dispersion correction is multiplied my the number of processes (I found this after taking a closer look at my md.log files to see where the energy was changing)! I guess this means I should use the serial version for meaningful binding energies. It also looks like it will be fixed for version 4.5.6 Thank you again, I really appreciate your help. Steve On 30/05/2012 9:42 PM, Stephen Cox wrote: Hi Justin, Thanks for getting back and posting the links. On 5/29/12 6:22 AM, Stephen Cox wrote: Hi, I'm running a number of energy minimizations on a clathrate supercell and I get quite significantly different values for the total energy depending on the number of mpi processes / number of threads I use. More specifically, some numbers I get are: #cores energy 1-2.41936409202696e+04 2-2.43726425776809e+04 3-2.45516442350804e+04 4-2.47003944216983e+04 #threadsenergy 1-2.41936409202696e+04 2-2.43726425776792e+04 3-2.45516442350804e+04 4-2.47306458924815e+04 I'd expect some numerical noise, but these differences seem to0 large for that. The difference is only 2%, which by MD standards, is quite good, I'd say ;) Consider the discussion here: I agree for MD this wouldn't be too bad, but I'd expect energy minimization to get very close to the same local minimum from a given starting configuration. The thing is I want to compute a binding curve for my clathrate and compare to DFT values for the binding energy (amongst other things), and the difference in energy between different number of cores is rather significant for this purpose. Given the usual roughness of the PE surface to which you are minimizing, some variation in end point is expected. Furthermore, if I only calculate the energy for nsteps = 0 (i.e. a single point energy for identical structures) I get the same trend as above (both mpi/openmp with domain/particle decomposition). Surely there shouldn't be such a large difference in energy for a single point calculation? nsteps = 0 is not strictly a single-point energy, since the constraints act before EM step 0. mdrun -s -rerun will give a single point. This probably won't change your observations. You should also be sure you're making observations with the latest release (4.5.5). If you can continue to observe this trend for more processors (overallocating?), then you may have evidence of a problem - but a full system description and an .mdp file will be in order also. Mark http://www.gromacs.org/Documentation/Terminology/Reproducibility To an extent, the information here may also be relevant: http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation Before submitting a bug report, I'd like to check: a) if someone has seen something similar; Sure. Energies can be different due to a whole host of factors (discussed above), and MPI only complicates matters. b) should I just trust the serial version? Maybe, but I don't know that there's evidence to say that any of the above tests are more or less accurate than the others. What happens if you run with mdrun -reprod on all your tests? Running with -reprod produces the same trend as above. If it was numerical noise, I would have thought that the numbers would fluctuate around some average value, not follow a definite trend where the energy decreases with the number of cores/threads... c) have I simply done something stupid (grompp.mdp appended below); Nope, looks fine. -Justin Thanks again for getting back to me. -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20120530/a4ed4a18/attachment-0001.html -- Message: 2 Date: Wed, 30 May 2012 07:51:02 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Re: Possible bug: energy changes with the number of nodes for energy minimization To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4fc609a6.4090...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 5/30/12 7:42 AM, Stephen Cox wrote: Hi Justin, Thanks for getting back and posting the links. On 5/29/12 6:22 AM, Stephen Cox wrote: Hi, I'm running a number of energy minimizations on a clathrate supercell and I get quite significantly
[gmx-users] Re: dangling bond at at one of the terminal ends
my fault, when i ran gromacs to produce topology file for a nucleotide sequence it is showing the above error There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. i tried giving the starting and ending residues in .n.tdb and .c.tdb files but it did not work with an error saying Fatal error: reading termini database: directive expected before line: P am uploading my PDB file of my DNA-protein compex sequence in which the nucleotide sequence ranges from 1 to 12216 http://gromacs.5086.n6.nabble.com/file/n4997914/dnaseq_rot1.pdb dnaseq_rot1.pdb -- View this message in context: http://gromacs.5086.n6.nabble.com/angling-bond-at-at-one-of-the-terminal-ends-tp4997894p4997914.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] mutational analyses: Cystine and indels
Hi Gromacs list, I would like to study two different mutations in a protein molecule, perhaps using MD. One of them is a insert deletion and the other is a mutation to Cys beside an existing Cys. The problem is that most of the molecular modeling programs, including Rosetta, do not handle with indels nor with cystine residues. Such deletion is located in a helix so as the molecular modeling program should be capable of moving a entire helix and rotate one or both parts it. That's not something trivial! The other mutation sounds worse. Rosetta can't even deal with mutation to Cys. Assuming that such mutation is not going to disrupt the protein folding, it probably will form a cystine residue. Not only because of the distance between cysteines, but also because the pH of the crystallization conditions. My question is: has anybody managed such kinds of mutations? or perhaps, could someone shade some light on these problems? All the best, Fred -- 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] mutational analyses: Cystine and indels
You might be able to use MODELLER for generating the helix deletions since it is alignment-based. If you use automodel.make(exit_stage=2) it will generate coordinates based on the specified sequence-spatial alignment but will stop there (otherwise it will try to run simulated annealing in vacuum). So what it will do is overlay the sideschains in your new sequence over the backbone of your beginning structure. You can then parameterize and refine with gromacs. Distance/angle restraints will be your friend here (set up distance restraints between N-H to keep the helix intact while you run energy minimzation and short relaxation MD). You are correct in that point indels that do not remove or add a full turn to the helix will be pretty drastic, so you will obviously have to find some ways to do validation, particularly when assessing if vicinal CYS will form disulfide bridge or not (which will also obviously do things to helix geometry) but I think these are hypotheses still well suited for MD to probe. On 2012-05-30 03:10:39PM -0300, Frederico Moras Ferreira wrote: Hi Gromacs list, I would like to study two different mutations in a protein molecule, perhaps using MD. One of them is a insert deletion and the other is a mutation to Cys beside an existing Cys. The problem is that most of the molecular modeling programs, including Rosetta, do not handle with indels nor with cystine residues. Such deletion is located in a helix so as the molecular modeling program should be capable of moving a entire helix and rotate one or both parts it. That's not something trivial! The other mutation sounds worse. Rosetta can't even deal with mutation to Cys. Assuming that such mutation is not going to disrupt the protein folding, it probably will form a cystine residue. Not only because of the distance between cysteines, but also because the pH of the crystallization conditions. My question is: has anybody managed such kinds of mutations? or perhaps, could someone shade some light on these problems? All the best, Fred -- 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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 with plumed version of gromacs in replica exchange
Dear Users , I am trying to use PLUMED with gromacs4.5.4 to perform umbrella sampling simulation using replica exchange as implemented within gromacs. I am using radius of gyration as the collective variable along which umbrella sampling is being performed. However, I find that whenever I try to run replica exchange with umbrella sampling using the plumed compiled gromacs, it always crashes saying that The properties of the 23 systems are all the same, there is nothing to exchange For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors; I had generated 23 replica each corresponding to a particular temperature and then used grompp (compiled using plumed ) to generate 23 .tpr file. Now, I use only one plumed.dat file . But, running the simulation using command ~/UTIL/OPENMPI/bin/mpirun -np 46 mdrun_plumed_s -multi 23 -replex 500 -s hremd -plumed plumed_umb.dat log_replica But, it ctashes.. I have also tried running regular replica exchange simulation without this plumed.dat file and then again it crashes saying the same error that it finds all replica identical. However, same simulation with official gromacs 4.5.4 executable ( i.e without the plumed plugin) runs without any problem. Also, the plumed plugin works great for a single temperature simulation. So, I wonder whether the plumed plugin is causing any trouble in running replica exchange simulation or I am missing something. Thanks in advance for help Sanku -- 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] Thermodynamic Integration Glu - Ala Mutation
Dear Gromacs Users, I am trying to find out the relative free energy difference of binding of a ligand with wild type protein (Glutamate residue) and mutant protein (Alanine residue). For charge part of the mutation, this is what I'm planning to do: ; residue 40 GLU rtp GLU q -1.0 552 opls_238 40GLU N 191 -0.514.0067 opls_238-0.5 14.0067 ; qtot 0.5 553 opls_241 40GLU H 1910.3 1.008 opls_241 0.3 1.008 ; qtot 0.8 554 opls_224B 40GLU CA191 0.14 12.011 opls_224B0.14 12.011 ; qtot 0.94 555 opls_140 40GLU HA191 0.06 1.008 opls_140 0.061.008 ; qtot 1 556 opls_136 40GLU CB192 -0.12 12.011 opls_135 -0.18 12.011 ; qtot 0.88 557 opls_140 40GLUHB1192 0.06 1.008 opls_140 0.061.008 ; qtot 0.94 558 opls_140 40GLUHB2192 0.06 1.008 opls_140 0.061.008 ; qtot 1 559 opls_274 40GLU CG193 -0.22 12.011 opls_140 0.061.008 ; qtot 0.78 560 opls_140 40GLUHG1193 0.06 1.008 DUM_1400.0 1.008 ; qtot 0.84 561 opls_140 40GLUHG2193 0.06 1.008 DUM_1400.0 1.008 ; qtot 0.9 562 opls_271 40GLU CD 1940.7 12.011 DUM_2710.0 12.011 ; qtot 1.6 563 opls_272 40GLUOE1194 -0.815.9994 DUM_272 0.0 15.9994 ; qtot 0.8 564 opls_272 40GLUOE2194 -0.815.9994 DUM_2720.0 15.9994 ; qtot 0 565 opls_235 40GLU C 1950.5 12.011 opls_235 0.5 12.011 ; qtot 0.5 566 opls_236 40GLU O 195 -0.515.9994 opls_236-0.515.9994 ; qtot 0 I added the DUM_140, DUM_271,DUM_272 atomtypes in ffnonbonded.itp. Further I added the bondtypes, angletypes and dihedraltypes in ffbonded.itp for state B. In order to maintain the electroneutrality, I am mutating a K+ ion to dummy as well. For the K+ going to dummy, I added a DUM_408 atomtype as well. *The questions I have are as follows:* *During the charge mutation will my dummy atoms have sigma and epsilon as 0.0? Since Ala residue does not have Cgamma, Cdelta and the oxygen as well as the Hgamma, all the dummy atoms should have sigma and epsilon as zero. Am I correct for this assumption?* *Further as I am mutating one ion, I dont want the mutating ion to come close to other ions (I have three K+ ions as my protein has -3 charge) as well as the protein atoms. Hence I'm having position restraints on the three ions. * *For the ion that is mutating to dummy, should I have have position restraints on dummy atom as well for the B state topology?* The section of topology for the K+ going to dummy is as follows: [ moleculetype ] ; Namenrexcl KM 1 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls-408 1 KMKM1 139.0983 DUM_408 0.0 39.0983 #ifdef POSRES_ION ; Position restraint for each Potassium ion [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 0 0 0 #endif Here I defined the KM as K+ that will go to dummy and other two K+ ions are represented as regular K+ ions. I'm pasting the regular K+ ion part of the topology below. [ moleculetype ] ; Namenrexcl K 1 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_408 1 K K1 139.0983 #ifdef POSRES_ION ; Position restraint for each Potassium ion [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif Let me know if you need more information. Thanks for your time, Regards Sai -- 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] mutational analyses: Cystine and indels
Hi Peter, Thanks for helping. I might not have been clear. The cys mutation is in a different location of the indel. I'm particularly worried about how the molecular modelling programs will treat indels. Several things can happen upon deletion of an helix residue. In this context, just take the structural information of the experimental model may not be something reliable. Em 30-05-2012 17:37, Peter C. Lai escreveu: You might be able to use MODELLER for generating the helix deletions since it is alignment-based. If you use automodel.make(exit_stage=2) it will generate coordinates based on the specified sequence-spatial alignment but will stop there (otherwise it will try to run simulated annealing in vacuum). So what it will do is overlay the sideschains in your new sequence over the backbone of your beginning structure. You can then parameterize and refine with gromacs. Distance/angle restraints will be your friend here (set up distance restraints between N-H to keep the helix intact while you run energy minimzation and short relaxation MD). You are correct in that point indels that do not remove or add a full turn to the helix will be pretty drastic, so you will obviously have to find some ways to do validation, particularly when assessing if vicinal CYS will form disulfide bridge or not (which will also obviously do things to helix geometry) but I think these are hypotheses still well suited for MD to probe. On 2012-05-30 03:10:39PM -0300, Frederico Moras Ferreira wrote: Hi Gromacs list, I would like to study two different mutations in a protein molecule, perhaps using MD. One of them is a insert deletion and the other is a mutation to Cys beside an existing Cys. The problem is that most of the molecular modeling programs, including Rosetta, do not handle with indels nor with cystine residues. Such deletion is located in a helix so as the molecular modeling program should be capable of moving a entire helix and rotate one or both parts it. That's not something trivial! The other mutation sounds worse. Rosetta can't even deal with mutation to Cys. Assuming that such mutation is not going to disrupt the protein folding, it probably will form a cystine residue. Not only because of the distance between cysteines, but also because the pH of the crystallization conditions. My question is: has anybody managed such kinds of mutations? or perhaps, could someone shade some light on these problems? All the best, Fred -- 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] Calculating the average separation between two multi-atom groups
Hi, I have a system in a slab geometry. A surface exists at z = 0; many hydrogens protrude from the surface, and these hydrogens are mostly (but not precisely) immobile. Above the surface, there is liquid, including the anion BF4- (tetrahedral arrangement of fluorines around a central boron). The liquid region is large, extending far from the surface, (far above the surface, the liquid behaves like liquid in the bulk). There is hydrogen-like bonding between the hydrogens protruding from the surface and the fluorines in BF4-. I would like to calculate the average H-F distance, where H atoms protrude from the stationary surface and F atoms exist on the BF4- ions. But saying that I want to compute the average H-F distance is very vague. I can think of at least two possible, hopefully reasonable, ways to formulate the problem: (i) For the purpose of calculating the average H-F separation, only consider fluorines on BF4- ions which are within a certain perpendicular distance z0 from the surface. In other words, consider the BF4- ions which lie in the region 0 z z0 (where z0 is positive and very small compared to the z dimension of the simulation box). Then, using those BF4- ions, I calculate the (time-averaged) H-F separation. (ii) For the purpose of calculating the average H-F separation, only consider fluorines when they are a certain small distance from any hydrogen. Are (i) or (ii) these feasible? For (i), I can think about using g_select to select BF4- ions which are a distance of z0 or less from the surface at z = 0. Maybe I would use a selection like 'res_com of resname BF4 and z 10' (where z0 = 10). The problem with this is that, I think, I would obtain an index file for each simulation timestep. So, I guess then if I have 200,000 simulation timesteps, I would have to run g_bond 200,000 times! (Or would g_dist be appropriate here?) Also, even my formulation in (i) is a little awkward; fluorines at one edge of the xy dimension would be far from hydrogens immobilized at the other side of the xy dimension, so I would get artifacts. For (ii), it seems that g_hbond might be useful. However, it does not seem that fluorine is currently implemented as a hydrogen bond acceptor for use in g_hbond. I have never attempted to modify the Gromacs code and I am not sure how easy this would be. But if H-F is a hydrogen-like bond, then (average) H-F bond length is what I am going after, I guess. Do you know of any recipes with which to do this, or do you have any suggestions? Thanks so much! Andrew DeYoung Carnegie Mellon University -- 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
