Re: [gmx-users] a new GROMACS simulation tool
Dear Kevin, I'm Gloria Saracino from the Center of Nanomedicine and Tissue Engineering of the Hospital of Niguarda Ca' Granda in Milan, Italy. I'm interested into knowing more about this new web based toolas I use MD everyday. Let me know what I have to do. Regards, Gloria Saracino Da: Kevin Chen fch6...@gmail.com A: 'Discussion list for GROMACS users' gmx-users@gromacs.org Inviato: Martedì 22 Ottobre 2013 16:34 Oggetto: [gmx-users] a new GROMACS simulation tool Hi Everyone, I'm writing to let you guys know that we have developed a web-based tool MD simulation tool for GROMACS. It is a software package primarily developed for biological MD and offers a huge amount of possible options and settings for tailoring the simulations. Seamlessly integrated with newly developed GUI interfaces, the tool provides comprehensive setup, simulation, analysis and job submission tools. Most importantly, unlike other GROMACS GUI applications, user can actually run really simulations using the dedicated HPC resources. That been said, there's no proposal and installation required. This tool could be a great fit for both teaching and research projects. Users inexperienced in MD can work along prepared workflows, while experts may enjoy a significant relief from the tedium of typing and scripting. As for now, we'd like to invite people to participate in user testing on this newly developed tool. Let me know if you'd like to try it out. We will set up an account for you. Best Regards, Kevin Chen, Ph.D. Information Technology at Purdue (ITaP) West Lafayette, IN 47907-2108 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_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] Continuing runs from 4.5.4 in 4.6.3
On Oct 23, 2013 7:24 AM, rajat desikan rajatdesi...@gmail.com wrote: Hi, We recently had a software upgrade in our cluster from gromacs 4.5.4. to gromacs 4.6.3.. I need to continue an earlier simulation that had been run in 4.5.4. using the .cpt, .tpr and .mdp. Are there any issues with continuing these runs in 4.6.3.? Can I concatenate these trajectories for later analysis? This is not recommended. Even if it works, the trajectory is discontinuous, and the years of accumulated bug fixes, and complete re-implementation of the kernels in 4.6.3, are likely to make the discontinuity observable. Upgrading within a minor release (4.5.4 - 4.5.7, 4.6 - 4.6.3) is intended to work (modulo relevant bug fixes), but would still tend to make your reviewer nervous. Mark I notice that I cannot use a 4.6.3 .cpt and .tpr in 4.5.4. Any input will be appreciated. Thanks. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Box size increases in NPT
On Oct 23, 2013 5:34 AM, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: Hello, I am running a NPT simulation for cyclopropylchloride(1) in 50%water(100)+50%ethanol(100) using opls force field parameter . After equilibration box size increases from 20 A to 70 A. Really? Seems wildly unlikely to have occurred without crashing. Over what time span? How did you observe before and after? What densities do you measure? Mark I used the following mdp file. ; RUN CONTROL PARAMETERS = integrator = sd ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps = 5 ; number of steps for center of mass motion removal = nstcomm = 100 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 0 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 500 nstenergy= 100 ; Output frequency and precision for xtc file = nstxtcout= 5000 xtc-precision= 1000 ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ;OPTIONS FOR TEMPERATURE COUPLING tc_grps = system tau_t= 0.1 ref_t= 290;350 ;OPTIONS FOR PRESSURE COUPLING Pcoupl = berendsen tau_p= 0.5 compressibility = 4.5e-05 ref_p= 1.0 ; OPTIONS FOR BONDS = constraints = hbonds ; Type of constraint algorithm = constraint-algorithm = Lincs ; Do not constrain the start configuration = unconstrained-start = no ; Relative tolerance of shake = shake-tol= 0.0001 ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 12 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs-warnangle = 30 ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist= 0.9 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = pme ;rcoulomb-switch = 0 rcoulomb = 0.9 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r= 1 ; Method for doing Van der Waals = vdw-type = switch ; cut-off lengths= rvdw-switch = 0.8 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.1 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters = pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no ; Free energy control stuff free_energy = no Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Box size increases in NPT
If the job is not very parallel, it will not crash. It is better to preequilibrate in NVT beforehand. Cyclopropylchloride is probably a liquid at 290K, if the model is parametrized reasonably. So it should not phase-separate. Vitaly On Wed, Oct 23, 2013 at 11:29 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Oct 23, 2013 5:34 AM, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: Hello, I am running a NPT simulation for cyclopropylchloride(1) in 50%water(100)+50%ethanol(100) using opls force field parameter . After equilibration box size increases from 20 A to 70 A. Really? Seems wildly unlikely to have occurred without crashing. Over what time span? How did you observe before and after? What densities do you measure? Mark I used the following mdp file. ; RUN CONTROL PARAMETERS = integrator = sd ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps = 5 ; number of steps for center of mass motion removal = nstcomm = 100 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 0 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 500 nstenergy= 100 ; Output frequency and precision for xtc file = nstxtcout= 5000 xtc-precision= 1000 ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ;OPTIONS FOR TEMPERATURE COUPLING tc_grps = system tau_t= 0.1 ref_t= 290;350 ;OPTIONS FOR PRESSURE COUPLING Pcoupl = berendsen tau_p= 0.5 compressibility = 4.5e-05 ref_p= 1.0 ; OPTIONS FOR BONDS = constraints = hbonds ; Type of constraint algorithm = constraint-algorithm = Lincs ; Do not constrain the start configuration = unconstrained-start = no ; Relative tolerance of shake = shake-tol= 0.0001 ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 12 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs-warnangle = 30 ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist= 0.9 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = pme ;rcoulomb-switch = 0 rcoulomb = 0.9 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r= 1 ; Method for doing Van der Waals = vdw-type = switch ; cut-off lengths= rvdw-switch = 0.8 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.1 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters = pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no ; Free energy control stuff free_energy = no Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Box size increases in NPT
By crash I meant explode not DD is impossible. Explosions don't happen because of parallelism, they happen because the steps are too large for the size of the forces. The forces required to stably expand a box from 20A to 70A seem likely to be so large that I am very skeptical that you could design such a simulation to do this with a 1fs time step. Mark On Wed, Oct 23, 2013 at 11:39 AM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: If the job is not very parallel, it will not crash. It is better to preequilibrate in NVT beforehand. Cyclopropylchloride is probably a liquid at 290K, if the model is parametrized reasonably. So it should not phase-separate. Vitaly On Wed, Oct 23, 2013 at 11:29 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Oct 23, 2013 5:34 AM, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: Hello, I am running a NPT simulation for cyclopropylchloride(1) in 50%water(100)+50%ethanol(100) using opls force field parameter . After equilibration box size increases from 20 A to 70 A. Really? Seems wildly unlikely to have occurred without crashing. Over what time span? How did you observe before and after? What densities do you measure? Mark I used the following mdp file. ; RUN CONTROL PARAMETERS = integrator = sd ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps = 5 ; number of steps for center of mass motion removal = nstcomm = 100 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 0 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 500 nstenergy= 100 ; Output frequency and precision for xtc file = nstxtcout= 5000 xtc-precision= 1000 ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ;OPTIONS FOR TEMPERATURE COUPLING tc_grps = system tau_t= 0.1 ref_t= 290;350 ;OPTIONS FOR PRESSURE COUPLING Pcoupl = berendsen tau_p= 0.5 compressibility = 4.5e-05 ref_p= 1.0 ; OPTIONS FOR BONDS = constraints = hbonds ; Type of constraint algorithm = constraint-algorithm = Lincs ; Do not constrain the start configuration = unconstrained-start = no ; Relative tolerance of shake = shake-tol= 0.0001 ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 12 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs-warnangle = 30 ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist= 0.9 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = pme ;rcoulomb-switch = 0 rcoulomb = 0.9 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r= 1 ; Method for doing Van der Waals = vdw-type = switch ; cut-off lengths= rvdw-switch = 0.8 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.1 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters = pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no ; Free energy control stuff free_energy = no Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] a new GROMACS simulation tool
I also would like to try 2013/10/23 Gloria Saracino glos...@yahoo.it Dear Kevin, I'm Gloria Saracino from the Center of Nanomedicine and Tissue Engineering of the Hospital of Niguarda Ca' Granda in Milan, Italy. I'm interested into knowing more about this new web based toolas I use MD everyday. Let me know what I have to do. Regards, Gloria Saracino Da: Kevin Chen fch6...@gmail.com A: 'Discussion list for GROMACS users' gmx-users@gromacs.org Inviato: Martedì 22 Ottobre 2013 16:34 Oggetto: [gmx-users] a new GROMACS simulation tool Hi Everyone, I'm writing to let you guys know that we have developed a web-based tool MD simulation tool for GROMACS. It is a software package primarily developed for biological MD and offers a huge amount of possible options and settings for tailoring the simulations. Seamlessly integrated with newly developed GUI interfaces, the tool provides comprehensive setup, simulation, analysis and job submission tools. Most importantly, unlike other GROMACS GUI applications, user can actually run really simulations using the dedicated HPC resources. That been said, there's no proposal and installation required. This tool could be a great fit for both teaching and research projects. Users inexperienced in MD can work along prepared workflows, while experts may enjoy a significant relief from the tedium of typing and scripting. As for now, we'd like to invite people to participate in user testing on this newly developed tool. Let me know if you'd like to try it out. We will set up an account for you. Best Regards, Kevin Chen, Ph.D. Information Technology at Purdue (ITaP) West Lafayette, IN 47907-2108 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] TFE-water simulation
Hi all, I have never performed TFE-water simulation therfore I want to know after inserting the peptide in the pre-equilibrated TFE-water mixture, do we need to adjust the number of TFE or water molecules ? or should I directly add ions to this system and run the production run. Any suggestion is welcome. Thank you. -- Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- 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] Continuing runs from 4.5.4 in 4.6.3
Thank you, Mark! On Wed, Oct 23, 2013 at 2:56 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Oct 23, 2013 7:24 AM, rajat desikan rajatdesi...@gmail.com wrote: Hi, We recently had a software upgrade in our cluster from gromacs 4.5.4. to gromacs 4.6.3.. I need to continue an earlier simulation that had been run in 4.5.4. using the .cpt, .tpr and .mdp. Are there any issues with continuing these runs in 4.6.3.? Can I concatenate these trajectories for later analysis? This is not recommended. Even if it works, the trajectory is discontinuous, and the years of accumulated bug fixes, and complete re-implementation of the kernels in 4.6.3, are likely to make the discontinuity observable. Upgrading within a minor release (4.5.4 - 4.5.7, 4.6 - 4.6.3) is intended to work (modulo relevant bug fixes), but would still tend to make your reviewer nervous. Mark I notice that I cannot use a 4.6.3 .cpt and .tpr in 4.5.4. Any input will be appreciated. Thanks. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy minimizations taking really, really long?
On 10/22/13 9:57 PM, Nimmy McNimmerson wrote: I have some simulations of inserting a probe molecule into a bilayer. Some molecules work fine. However, a certain class of molecules is taking an absurdly long time to run the exact same simulation, even though I energy minimized the molecules individually beforehand and there are no overlaps. What might be going wrong? Please clarify - your subject line says the EM is taking a long time, but the content here suggests the post-EM simulation process is the problem. Which is it? Are you sure the .mdp files were identical? Small changes can have big effects on performance. Are you sure the hardware is fully functional? A stuck node or lagging file system can explain slow runs. If mdrun is still churning along without crashing, most likely the problem is external. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] TFE-water simulation
On 10/23/13 7:20 AM, Archana Sonawani-Jagtap wrote: Hi all, I have never performed TFE-water simulation therfore I want to know after inserting the peptide in the pre-equilibrated TFE-water mixture, do we need to adjust the number of TFE or water molecules ? That depends on how you constructed the system. genbox will not automatically update the number of TFE, but it can update the number of water molecules if you chose the proper command-line option. Regardless, the [molecules] section of the .top must accurately reflect the contents of the configuration in terms of order and number of molecules. Simple grep statements will let you count how many of each are present. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] a new GROMACS simulation tool
me to On Wed, Oct 23, 2013 at 12:27 PM, Thales Kronenberger kronenberg...@gmail.com wrote: I also would like to try 2013/10/23 Gloria Saracino glos...@yahoo.it Dear Kevin, I'm Gloria Saracino from the Center of Nanomedicine and Tissue Engineering of the Hospital of Niguarda Ca' Granda in Milan, Italy. I'm interested into knowing more about this new web based toolas I use MD everyday. Let me know what I have to do. Regards, Gloria Saracino Da: Kevin Chen fch6...@gmail.com A: 'Discussion list for GROMACS users' gmx-users@gromacs.org Inviato: Martedì 22 Ottobre 2013 16:34 Oggetto: [gmx-users] a new GROMACS simulation tool Hi Everyone, I'm writing to let you guys know that we have developed a web-based tool MD simulation tool for GROMACS. It is a software package primarily developed for biological MD and offers a huge amount of possible options and settings for tailoring the simulations. Seamlessly integrated with newly developed GUI interfaces, the tool provides comprehensive setup, simulation, analysis and job submission tools. Most importantly, unlike other GROMACS GUI applications, user can actually run really simulations using the dedicated HPC resources. That been said, there's no proposal and installation required. This tool could be a great fit for both teaching and research projects. Users inexperienced in MD can work along prepared workflows, while experts may enjoy a significant relief from the tedium of typing and scripting. As for now, we'd like to invite people to participate in user testing on this newly developed tool. Let me know if you'd like to try it out. We will set up an account for you. Best Regards, Kevin Chen, Ph.D. Information Technology at Purdue (ITaP) West Lafayette, IN 47907-2108 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Continuing runs from 4.5.4 in 4.6.3
There shouldn't be a problem for that. BTW, can you also enter a ticket at Daigrid.org for this matter? Thanks -Kevin -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of rajat desikan Sent: Wednesday, October 23, 2013 1:24 AM To: Discussion list for GROMACS users Subject: [gmx-users] Continuing runs from 4.5.4 in 4.6.3 Hi, We recently had a software upgrade in our cluster from gromacs 4.5.4. to gromacs 4.6.3.. I need to continue an earlier simulation that had been run in 4.5.4. using the .cpt, .tpr and .mdp. Are there any issues with continuing these runs in 4.6.3.? Can I concatenate these trajectories for later analysis? I notice that I cannot use a 4.6.3 .cpt and .tpr in 4.5.4. Any input will be appreciated. Thanks. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] a new GROMACS simulation tool
Hi, Sounds very interesting. Can I have a test account, please? The Lindahl group has some related work going on at http://copernicus-computing.org/, automating large-scale simulation workflows. I'm not sure yet whether we have any synergies! :-) Cheers, Mark On Tue, Oct 22, 2013 at 4:34 PM, Kevin Chen fch6...@gmail.com wrote: Hi Everyone, I'm writing to let you guys know that we have developed a web-based tool MD simulation tool for GROMACS. It is a software package primarily developed for biological MD and offers a huge amount of possible options and settings for tailoring the simulations. Seamlessly integrated with newly developed GUI interfaces, the tool provides comprehensive setup, simulation, analysis and job submission tools. Most importantly, unlike other GROMACS GUI applications, user can actually run really simulations using the dedicated HPC resources. That been said, there's no proposal and installation required. This tool could be a great fit for both teaching and research projects. Users inexperienced in MD can work along prepared workflows, while experts may enjoy a significant relief from the tedium of typing and scripting. As for now, we'd like to invite people to participate in user testing on this newly developed tool. Let me know if you'd like to try it out. We will set up an account for you. Best Regards, Kevin Chen, Ph.D. Information Technology at Purdue (ITaP) West Lafayette, IN 47907-2108 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] a new GROMACS simulation tool
Hi Kevin, It seems interesting. I would like to try it out. May I have an account? Best regards, Ehsan - Original Message - From: Kevin Chen fch6...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, October 22, 2013 7:34:10 AM Subject: [gmx-users] a new GROMACS simulation tool Hi Everyone, I'm writing to let you guys know that we have developed a web-based tool MD simulation tool for GROMACS. It is a software package primarily developed for biological MD and offers a huge amount of possible options and settings for tailoring the simulations. Seamlessly integrated with newly developed GUI interfaces, the tool provides comprehensive setup, simulation, analysis and job submission tools. Most importantly, unlike other GROMACS GUI applications, user can actually run really simulations using the dedicated HPC resources. That been said, there's no proposal and installation required. This tool could be a great fit for both teaching and research projects. Users inexperienced in MD can work along prepared workflows, while experts may enjoy a significant relief from the tedium of typing and scripting. As for now, we'd like to invite people to participate in user testing on this newly developed tool. Let me know if you'd like to try it out. We will set up an account for you. Best Regards, Kevin Chen, Ph.D. Information Technology at Purdue (ITaP) West Lafayette, IN 47907-2108 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] a new GROMACS simulation tool
Please could I have an account too. Hi Everyone, I'm writing to let you guys know that we have developed a web-based tool MD simulation tool for GROMACS. It is a software package primarily developed for biological MD and offers a huge amount of possible options and settings for tailoring the simulations. Seamlessly integrated with newly developed GUI interfaces, the tool provides comprehensive setup, simulation, analysis and job submission tools. Most importantly, unlike other GROMACS GUI applications, user can actually run really simulations using the dedicated HPC resources. That been said, there's no proposal and installation required. This tool could be a great fit for both teaching and research projects. Users inexperienced in MD can work along prepared workflows, while experts may enjoy a significant relief from the tedium of typing and scripting. As for now, we'd like to invite people to participate in user testing on this newly developed tool. Let me know if you'd like to try it out. We will set up an account for you. Best Regards, Kevin Chen, Ph.D. Information Technology at Purdue (ITaP) West Lafayette, IN 47907-2108 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] a new GROMACS simulation tool
I'd like to check it out too On Wed, Oct 23, 2013 at 8:45 AM, Ehsan Sadeghi es...@sfu.ca wrote: Hi Kevin, It seems interesting. I would like to try it out. May I have an account? Best regards, Ehsan - Original Message - From: Kevin Chen fch6...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, October 22, 2013 7:34:10 AM Subject: [gmx-users] a new GROMACS simulation tool Hi Everyone, I'm writing to let you guys know that we have developed a web-based tool MD simulation tool for GROMACS. It is a software package primarily developed for biological MD and offers a huge amount of possible options and settings for tailoring the simulations. Seamlessly integrated with newly developed GUI interfaces, the tool provides comprehensive setup, simulation, analysis and job submission tools. Most importantly, unlike other GROMACS GUI applications, user can actually run really simulations using the dedicated HPC resources. That been said, there's no proposal and installation required. This tool could be a great fit for both teaching and research projects. Users inexperienced in MD can work along prepared workflows, while experts may enjoy a significant relief from the tedium of typing and scripting. As for now, we'd like to invite people to participate in user testing on this newly developed tool. Let me know if you'd like to try it out. We will set up an account for you. Best Regards, Kevin Chen, Ph.D. Information Technology at Purdue (ITaP) West Lafayette, IN 47907-2108 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] pbc problem
Dear gromacs users My system contains DOPC + CHOLESTEROLO + WATER + drug molecules in a rectangular box. I put drug molecule in 2 position: a) drug in the center of bilayer membrane, b) drug inside water molecules in top leaflet. For both positions, I did energy minimization successfully with following mdp file. -- ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom nstlist= 1; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions --- After energy minimization, I saw obtained file (em.gro) by VMD. All things were true and intact. For both positions, I did equilibration in NPT ensemble with following mdp file. --- ; Run parameters integrator= md; leap-frog integrator nsteps= 25; 2 * 50 = 1000 ps (1 ns) dt= 0.002; 2 fs ; Output control nstxout= 100; save coordinates every 0.2 ps nstvout= 100; save velocities every 0.2 ps nstxtcout = 100; xtc compressed trajectory output every 2 ps nstenergy= 100; save energies every 0.2 ps nstlog= 100; update log file every 0.2 ps energygrps = CHOL DOPC drg SOL ; Bond parameters continuation= no; Restarting after NVT constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cels nstlist= 5; 10 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; More accurate thermostat tc-grps= CHOL_DOPCdrg SOL; three coupling groups - more accurate tau_t= 0.50.5 0.5 ; time constant, in ps ref_t= 323 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Parrinello-Rahman; Pressure coupling on in NPT pcoupltype= semiisotropic; uniform scaling of x-y box vectors, independent z tau_p= 5.0; time constant, in ps ref_p= 1.01.0; reference pressure, x-y, z (in bar) compressibility = 4.5e-54.5e-5; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= yes; assign velocities from Maxwell distribution gen_temp= 323; temperature for Maxwell distribution gen_seed= -1; generate a random seed ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = CHOL_DOPC_drg SOL ; Scale COM of reference coordinates refcoord_scaling = com --- For 2 positions, I chechked tempreture and pressure fluctuation and box dimention during equilibration. All things were good. When I saw trajectory by VMD (npt.gro and npt xtc), I had pbc problem (some atoms leave box and enter the box in opposit direction). For position (a): I corrected pbc problem by trjconv -f npt.xtc -s npt.tpr -n index.ndx -o 2npt.xtc -pbc mol -center I selected CHOL_DOPC-drg group for centering. So problem was solved, approximately. For position (b) in which drug
Re: [gmx-users] a new GROMACS simulation tool
Hi Kevin I would like to try it out.. Let me know the procedure to create an account.. Regards Ash On Tuesday, October 22, 2013, Kevin Chen wrote: Hi Everyone, I'm writing to let you guys know that we have developed a web-based tool MD simulation tool for GROMACS. It is a software package primarily developed for biological MD and offers a huge amount of possible options and settings for tailoring the simulations. Seamlessly integrated with newly developed GUI interfaces, the tool provides comprehensive setup, simulation, analysis and job submission tools. Most importantly, unlike other GROMACS GUI applications, user can actually run really simulations using the dedicated HPC resources. That been said, there's no proposal and installation required. This tool could be a great fit for both teaching and research projects. Users inexperienced in MD can work along prepared workflows, while experts may enjoy a significant relief from the tedium of typing and scripting. As for now, we'd like to invite people to participate in user testing on this newly developed tool. Let me know if you'd like to try it out. We will set up an account for you. Best Regards, Kevin Chen, Ph.D. Information Technology at Purdue (ITaP) West Lafayette, IN 47907-2108 -- gmx-users mailing listgmx-users@gromacs.org javascript:; 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 javascript:;. * 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] Re: a new GROMACS simulation tool
Sound nice. I would like to try out. Could You please set up an account for me? Regards, Eduardo Villarreal villarea...@hss.edu - Eduardo Villarreal Ramírez Postdoctoral Research Fellow Mineralized Tissue Laboratory, Hospital for Special Surgery. -- View this message in context: http://gromacs.5086.x6.nabble.com/a-new-GROMACS-simulation-tool-tp5011910p5011934.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] Re: a new GROMACS simulation tool
Hi Kevin Can I have a try? Best Houyang On Wed, Oct 23, 2013 at 12:30 PM, Villarealed villarea...@hss.edu wrote: Sound nice. I would like to try out. Could You please set up an account for me? Regards, Eduardo Villarreal villarea...@hss.edu - Eduardo Villarreal Ramírez Postdoctoral Research Fellow Mineralized Tissue Laboratory, Hospital for Special Surgery. -- View this message in context: http://gromacs.5086.x6.nabble.com/a-new-GROMACS-simulation-tool-tp5011910p5011934.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 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] list
Sorry, i should want to be delete my contact from mailing list. thanks -- 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] list
On 10/23/13 12:44 PM, Michelangelo Scordino wrote: Sorry, i should want to be delete my contact from mailing list. thanks Unsubscribing is explained in the footer of every email that hits the list: * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Aw: RE: [gmx-users] Continuing runs from 4.5.4 in 4.6.3
I ran into this, you basically should determine your time frame, and install 4.5.4 if its a problem local (only 1-2 hours), to finish the work, otherwise you need to start from scratch. But I did this with older versions, so do not know about higher versions (such as if theprogrammerseliminated the read version number thing at many of the script initializing things...). The auxillary software does work for analysis, but you end up having to cut things into portions with some aspects, 1/2 one version versus 1/2 the other...but mostly for higher end analysis, not the simplistic ones, such as distance versus hessian matrices or covariance. Stephan Watkins Gesendet:Mittwoch, 23. Oktober 2013 um 16:17 Uhr Von:Kevin Chen fch6...@gmail.com An:Discussion list for GROMACS users gmx-users@gromacs.org Betreff:RE: [gmx-users] Continuing runs from 4.5.4 in 4.6.3 There shouldnt be a problem for that. BTW, can you also enter a ticket at Daigrid.org for this matter? Thanks -Kevin -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of rajat desikan Sent: Wednesday, October 23, 2013 1:24 AM To: Discussion list for GROMACS users Subject: [gmx-users] Continuing runs from 4.5.4 in 4.6.3 Hi, We recently had a software upgrade in our cluster from gromacs 4.5.4. to gromacs 4.6.3.. I need to continue an earlier simulation that had been run in 4.5.4. using the .cpt, .tpr and .mdp. Are there any issues with continuing these runs in 4.6.3.? Can I concatenate these trajectories for later analysis? I notice that I cannot use a 4.6.3 .cpt and .tpr in 4.5.4. Any input will be appreciated. Thanks. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappas Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pbc problem
I usually use -pbc nojump for my protein simulations and this works every time. Dear gromacs users My system contains DOPC + CHOLESTEROLO + WATER + drug molecules in a rectangular box. I put drug molecule in 2 position: a) drug in the center of bilayer membrane, b) drug inside water molecules in top leaflet. For both positions, I did energy minimization successfully with following mdp file. -- ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom nstlist= 1; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions --- After energy minimization, I saw obtained file (em.gro) by VMD. All things were true and intact. For both positions, I did equilibration in NPT ensemble with following mdp file. --- ; Run parameters integrator= md; leap-frog integrator nsteps= 25; 2 * 50 = 1000 ps (1 ns) dt= 0.002; 2 fs ; Output control nstxout= 100; save coordinates every 0.2 ps nstvout= 100; save velocities every 0.2 ps nstxtcout = 100; xtc compressed trajectory output every 2 ps nstenergy= 100; save energies every 0.2 ps nstlog= 100; update log file every 0.2 ps energygrps = CHOL DOPC drg SOL ; Bond parameters continuation= no; Restarting after NVT constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cels nstlist= 5; 10 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; More accurate thermostat tc-grps= CHOL_DOPCdrg SOL; three coupling groups - more accurate tau_t= 0.50.5 0.5 ; time constant, in ps ref_t= 323 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Parrinello-Rahman; Pressure coupling on in NPT pcoupltype= semiisotropic; uniform scaling of x-y box vectors, independent z tau_p= 5.0; time constant, in ps ref_p= 1.01.0; reference pressure, x-y, z (in bar) compressibility = 4.5e-54.5e-5; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= yes; assign velocities from Maxwell distribution gen_temp= 323; temperature for Maxwell distribution gen_seed= -1; generate a random seed ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = CHOL_DOPC_drg SOL ; Scale COM of reference coordinates refcoord_scaling = com --- For 2 positions, I chechked tempreture and pressure fluctuation and box dimention during equilibration. All things were good. When I saw trajectory by VMD (npt.gro and npt xtc), I had pbc problem (some atoms leave box and enter the box in opposit direction). For position (a): I corrected pbc problem by
Re: [gmx-users] pbc problem
Center on a particular lipid? Or head group? Mark On Oct 23, 2013 6:13 PM, shahab shariati shahab.shari...@gmail.com wrote: Dear gromacs users My system contains DOPC + CHOLESTEROLO + WATER + drug molecules in a rectangular box. I put drug molecule in 2 position: a) drug in the center of bilayer membrane, b) drug inside water molecules in top leaflet. For both positions, I did energy minimization successfully with following mdp file. -- ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom nstlist= 1; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions --- After energy minimization, I saw obtained file (em.gro) by VMD. All things were true and intact. For both positions, I did equilibration in NPT ensemble with following mdp file. --- ; Run parameters integrator= md; leap-frog integrator nsteps= 25; 2 * 50 = 1000 ps (1 ns) dt= 0.002; 2 fs ; Output control nstxout= 100; save coordinates every 0.2 ps nstvout= 100; save velocities every 0.2 ps nstxtcout = 100; xtc compressed trajectory output every 2 ps nstenergy= 100; save energies every 0.2 ps nstlog= 100; update log file every 0.2 ps energygrps = CHOL DOPC drg SOL ; Bond parameters continuation= no; Restarting after NVT constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cels nstlist= 5; 10 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; More accurate thermostat tc-grps= CHOL_DOPCdrg SOL; three coupling groups - more accurate tau_t= 0.50.5 0.5 ; time constant, in ps ref_t= 323 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Parrinello-Rahman; Pressure coupling on in NPT pcoupltype= semiisotropic; uniform scaling of x-y box vectors, independent z tau_p= 5.0; time constant, in ps ref_p= 1.01.0; reference pressure, x-y, z (in bar) compressibility = 4.5e-54.5e-5; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= yes; assign velocities from Maxwell distribution gen_temp= 323; temperature for Maxwell distribution gen_seed= -1; generate a random seed ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = CHOL_DOPC_drg SOL ; Scale COM of reference coordinates refcoord_scaling = com --- For 2 positions, I chechked tempreture and pressure fluctuation and box dimention during equilibration. All things were good. When I saw trajectory by VMD (npt.gro and npt xtc), I had pbc problem (some atoms leave box and enter the box in opposit direction). For
[gmx-users] converting pdb of protein+ATP+water+ion into gromacs files
Hello, I am trying to convert a protein+ATP+water+ion system pdb into gromacs files. I need to use the existing water and ion coordinates. I can convert the protein part using pdb2gmx and grompp fine. But, I do not know how to process the solvent and ion coordinates separately and combine them to make the final system. Can anyone give me direction? I am new to gromacs... Thanks you very much. -Dina -- 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] converting pdb of protein+ATP+water+ion into gromacs files
On 10/23/13 4:28 PM, Dina Mirijanian wrote: Hello, I am trying to convert a protein+ATP+water+ion system pdb into gromacs files. I need to use the existing water and ion coordinates. I can convert the protein part using pdb2gmx and grompp fine. But, I do not know how to process the solvent and ion coordinates separately and combine them to make the final system. Can anyone give me direction? I am new to gromacs... Copy and paste the coordinates into the pdb2gmx-processed coordinate file (note that you can keep .pdb format or convert to .gro easily with editconf). The solvent and ion topologies are #included in the pdb2gmx-produced topology already, you just need to update the [molecules] directive accordingly. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] converting pdb of protein+ATP+water+ion into gromacs files
got it. Thanks Justin. On Wed, Oct 23, 2013 at 4:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/23/13 4:28 PM, Dina Mirijanian wrote: Hello, I am trying to convert a protein+ATP+water+ion system pdb into gromacs files. I need to use the existing water and ion coordinates. I can convert the protein part using pdb2gmx and grompp fine. But, I do not know how to process the solvent and ion coordinates separately and combine them to make the final system. Can anyone give me direction? I am new to gromacs... Copy and paste the coordinates into the pdb2gmx-processed coordinate file (note that you can keep .pdb format or convert to .gro easily with editconf). The solvent and ion topologies are #included in the pdb2gmx-produced topology already, you just need to update the [molecules] directive accordingly. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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: a new GROMACS simulation tool
Hi, I also want to try :) Best regards, ~Thu On Wed, Oct 23, 2013 at 11:39 PM, houyang chen houyangc...@gmail.comwrote: Hi Kevin Can I have a try? Best Houyang On Wed, Oct 23, 2013 at 12:30 PM, Villarealed villarea...@hss.edu wrote: Sound nice. I would like to try out. Could You please set up an account for me? Regards, Eduardo Villarreal villarea...@hss.edu - Eduardo Villarreal Ramírez Postdoctoral Research Fellow Mineralized Tissue Laboratory, Hospital for Special Surgery. -- View this message in context: http://gromacs.5086.x6.nabble.com/a-new-GROMACS-simulation-tool-tp5011910p5011934.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 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] cant find certain atomtypes from atomtype database
dear gromacs users im using gromacs to make CS2 MD programs i made pdb file (by converting mol file to pdb file) and rtp file for CS2this is what i made pdb file COMPNDUNNAMEDAUTHORGENERATED BY OPEN BABEL 2.3.2HETATM1 C LIG 1 19.882 -4.263 -0.027 1.00 0.00 C HETATM2 S LIG 1 21.256 -5.103 -0.054 1.00 0.00 S HETATM3 S LIG 1 18.508 -3.424 0.000 1.00 0.00 S CONECT123 CONECT21 CONECT31 MASTER00000000 3030END - rtp file [ LIG ] [ atoms ]C opls_77 0 0S1 opls_202 0 0S2 opls_202 0 0 [ bonds ]C S1C S2 i attached rtp file to /usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp andi added it to residuetypes.dat (which is in /usr/share/gromacs/top)then i wrote command pdb2gmx to make gro file but it failed Fatal error:Atom type opls_77 (residue LIG) not found in atomtype databaseFor more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors before i made rtp file, i checked atomtypes atp file which is in oplsaa.ff it says olps_77 is carbon(isobutene) and opls_202 is sulfides i dont know why gromacs cant find atom type opls_77 also, to make rtp file how to give charge and charge group to each atoms? someone who knows about this, please help me thank you so much -- View this message in context: http://gromacs.5086.x6.nabble.com/cant-find-certain-atomtypes-from-atomtype-database-tp5011944.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
