[gmx-users] Re: Minimum distance periodic images, protein simulation
Hi Justin, Thanks for your reply. I have some follow-up questions. Since the simulation is high temperature (450 K) there is slight unfolding of the protein. The box was set up as rhombic dodecahedron with 1.2 nm as the distance between solute and edge of box. pdb2gmx -f 1L2Y.pdb -o 1L2Y-processed.gro -ignh -water spce The cutoffs are 0.9 nm for VDW and electrostatics. Do you suggest using an even bigger box for studying unfolding? Or is there something else that could be going on? Do you have any ball park suggestions for a good size of the box or is this something that I would have to experiment with different sizes until I land a suitable box. Thanks a lot, -- View this message in context: http://gromacs.5086.x6.nabble.com/Minimum-distance-periodic-images-protein-simulation-tp5011343p5011347.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: Minimum distance periodic images, protein simulation
You can try a run in implicit solvent to get a feel for the maximum diameter of the protein while unfolding. You will not have any certainty unless you can afford a box whose diameter is that of the straight-line peptide... Mark On Sat, Sep 21, 2013 at 1:03 PM, aksharma arunsharma_...@yahoo.com wrote: Hi Justin, Thanks for your reply. I have some follow-up questions. Since the simulation is high temperature (450 K) there is slight unfolding of the protein. The box was set up as rhombic dodecahedron with 1.2 nm as the distance between solute and edge of box. pdb2gmx -f 1L2Y.pdb -o 1L2Y-processed.gro -ignh -water spce The cutoffs are 0.9 nm for VDW and electrostatics. Do you suggest using an even bigger box for studying unfolding? Or is there something else that could be going on? Do you have any ball park suggestions for a good size of the box or is this something that I would have to experiment with different sizes until I land a suitable box. Thanks a lot, -- View this message in context: http://gromacs.5086.x6.nabble.com/Minimum-distance-periodic-images-protein-simulation-tp5011343p5011347.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
Re: [gmx-users] jwe1050i + jwe0019i errors = SIGSEGV (Fujitsu)
Dear Mark and the rest of the Gromacs team, Thanks a lot for your response. I have been trying to isolate the problem and have also been in discussion with the support staff. They suggested it may be a bug in the gromacs code, and I have tried to isolate the problem more precisely. Considering that the calculation is run under MPI with 16 OpenMP cores per MPI node, the error seems to occur under the following conditions: A few thousand atoms: 1 or 2 MPI nodes: OK Double the number of atoms (~15,000): 1 MPI node: OK, 2 MPI nodes: SIGSEGV error described below. So it seems that the error occurs for relatively large systems which use MPI. The crash mentions the calc_cell_indices function (see below). Is this somehow a problem with memory not being sufficient at the MPI interface at this function? I'm not sure how to proceed further. Any help would be greatly appreciated. Gromacs version is 4.6.3. Thank you very much for your time. James On 4 September 2013 16:05, Mark Abraham mark.j.abra...@gmail.com wrote: On Sep 4, 2013 7:59 AM, James jamesresearch...@gmail.com wrote: Dear all, I'm trying to run Gromacs on a Fujitsu supercomputer but the software is crashing. I run grompp: grompp_mpi_d -f parameters.mdp -c system.pdb -p overthe.top and it produces the error: jwe1050i-w The hardware barrier couldn't be used and continues processing using the software barrier. taken to (standard) corrective action, execution continuing. error summary (Fortran) error number error level error count jwe1050i w 1 total error count = 1 but still outputs topol.tpr so I can continue. There's no value in compiling grompp with MPI or in double precision. I then run with export FLIB_FASTOMP=FALSE source /home/username/Gromacs463/bin/GMXRC.bash mpiexec mdrun_mpi_d -ntomp 16 -v but it crashes: starting mdrun 'testrun' 5 steps, 100.0 ps. jwe0019i-u The program was terminated abnormally with signal number SIGSEGV. signal identifier = SEGV_MAPERR, address not mapped to object error occurs at calc_cell_indices._OMP_1 loc 00233474 offset 03b4 calc_cell_indices._OMP_1 at loc 002330c0 called from loc 02088fa0 in start_thread start_thread at loc 02088e4c called from loc 029d19b4 in __thread_start __thread_start at loc 029d1988 called from o.s. error summary (Fortran) error number error level error count jwe0019i u 1 jwe1050i w 1 total error count = 2 [ERR.] PLE 0014 plexec The process terminated abnormally.(rank=1)(nid=0x03060006)(exitstatus=240)(CODE=2002,1966080,61440) [ERR.] PLE The program that the user specified may be illegal or inaccessible on the node.(nid=0x03060006) Any ideas what could be wrong? It works on my local intel machine. Looks like it wasn't compiled correctly for the target machine. What was the cmake command, what does mdrun -version output? Also, if this is the K computer, probably we can't help, because the compiler docs are officially unavailable to us. National secret, and all ;-) Mark Thanks in advance, James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] jwe1050i + jwe0019i errors = SIGSEGV (Fujitsu)
On Sat, Sep 21, 2013 at 2:45 PM, James jamesresearch...@gmail.com wrote: Dear Mark and the rest of the Gromacs team, Thanks a lot for your response. I have been trying to isolate the problem and have also been in discussion with the support staff. They suggested it may be a bug in the gromacs code, and I have tried to isolate the problem more precisely. First, do the GROMACS regression tests for Verlet kernels pass? (Run them all, but those with nbnxn prefix are of interest here.) They likely won't scale to 16 OMP threads, but you can vary OMP_NUM_THREADS environment variable to see what you can see. Considering that the calculation is run under MPI with 16 OpenMP cores per MPI node, the error seems to occur under the following conditions: A few thousand atoms: 1 or 2 MPI nodes: OK Double the number of atoms (~15,000): 1 MPI node: OK, 2 MPI nodes: SIGSEGV error described below. So it seems that the error occurs for relatively large systems which use MPI. ~500 atoms per core (thread) is a system in the normal GROMACS scaling regime. 16 OMP threads is more than is useful on other HPC systems, but since we don't know what your hardware is, whether you are investigating something useful is your decision. The crash mentions the calc_cell_indices function (see below). Is this somehow a problem with memory not being sufficient at the MPI interface at this function? I'm not sure how to proceed further. Any help would be greatly appreciated. If there is a problem with GROMACS (which so far I doubt), we'd need a stack trace that shows a line number (rather than addresses) in order to start to locate it. Mark Gromacs version is 4.6.3. Thank you very much for your time. James On 4 September 2013 16:05, Mark Abraham mark.j.abra...@gmail.com wrote: On Sep 4, 2013 7:59 AM, James jamesresearch...@gmail.com wrote: Dear all, I'm trying to run Gromacs on a Fujitsu supercomputer but the software is crashing. I run grompp: grompp_mpi_d -f parameters.mdp -c system.pdb -p overthe.top and it produces the error: jwe1050i-w The hardware barrier couldn't be used and continues processing using the software barrier. taken to (standard) corrective action, execution continuing. error summary (Fortran) error number error level error count jwe1050i w 1 total error count = 1 but still outputs topol.tpr so I can continue. There's no value in compiling grompp with MPI or in double precision. I then run with export FLIB_FASTOMP=FALSE source /home/username/Gromacs463/bin/GMXRC.bash mpiexec mdrun_mpi_d -ntomp 16 -v but it crashes: starting mdrun 'testrun' 5 steps, 100.0 ps. jwe0019i-u The program was terminated abnormally with signal number SIGSEGV. signal identifier = SEGV_MAPERR, address not mapped to object error occurs at calc_cell_indices._OMP_1 loc 00233474 offset 03b4 calc_cell_indices._OMP_1 at loc 002330c0 called from loc 02088fa0 in start_thread start_thread at loc 02088e4c called from loc 029d19b4 in __thread_start __thread_start at loc 029d1988 called from o.s. error summary (Fortran) error number error level error count jwe0019i u 1 jwe1050i w 1 total error count = 2 [ERR.] PLE 0014 plexec The process terminated abnormally.(rank=1)(nid=0x03060006)(exitstatus=240)(CODE=2002,1966080,61440) [ERR.] PLE The program that the user specified may be illegal or inaccessible on the node.(nid=0x03060006) Any ideas what could be wrong? It works on my local intel machine. Looks like it wasn't compiled correctly for the target machine. What was the cmake command, what does mdrun -version output? Also, if this is the K computer, probably we can't help, because the compiler docs are officially unavailable to us. National secret, and all ;-) Mark Thanks in advance, James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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
[gmx-users] Use of walls combining with the PME and pressure coupling
Dear all, Im working on some simulations about the adsorption of protein on solid surfaces, which have slab geometry in the x-y plane. In order to reduce the amount of water molecules and at the same time to decrease the unphysical Coulomb interaction between periodic images in the z-direction, an empty layer should be added in the z-direction. To prevent the water molecules from evaporating into the vacuum layer, Im going to use the wall option. However, there are some details that Im not sure about. What are your suggestions about the choice of wall_atomtype and wall_type? Is it necessary to leave some room for the two walls (or it may lead to high interaction energies between the walls and the system) and how to determine its height (in my simulations, I leave about 1.5 , respectively)? Does it have something to do with the wall_atomtype and wall_type? When choose nwall=2, pressure coupling and Ewald summation can be used (it is usually best to use semi-isotropic pressure coupling with x/y compressibility set to 0). It means the wall can move in the z-direction? Can the pressure coupling be used in system with fixed atoms and how can we control/calculate the pressure of the mobile phase (as it has been discussed in the paper [Biointerphases 5, 85 (2010)] using the CHARMM package)? When combing walls with the PME method, it is suggested the eward_geometry be set to 3dc and the wall_eward_zfac be 3. Does this mean there will be an empty layer whose height is 3 times the slab height added to increase the z-dimension of the box? And Im not sure about the exact meaning of the slab height; it seems to be the length/width of the slab (as described in the paper [J. Chem. Phys.111, 3155 (1999)]). Im so sorry for troubling you with so many questions. But I need your help badly and sincerely. Anyone can help me? Thank you!! Bellow is an attachment of mdp file used in my simulation work. If there is anything wrong, please be kind to point it out. Thanks again! Chunwang Peng Room 302, Building 16， Chemistry Chemical Engineering， South China University of Technology， Tianhe District, Guangzhou md.mdp title = cyt-c on Au MD ; Run parameters integrator = md ; leap-frog integrator nsteps = 1000 ; 2 * 1000 = 2 ps, 20 ns dt = 0.002 ; 2 fs comm-mode = Linear ; mode for center of mass motion removal ; Output control nstxout = 1 ; save coordinates every 20 ps nstvout = 1 ; save velocities every 20 ps nstenergy = 1 ; save energies every 20 ps nstlog = 1 ; update log file every 20 ps ; Selection of energy groups energygrps = Protein_HEM GLD ;Group(s) to write to energy file ; Bond parameters continuation = yes ; Restarting after NPT constraint_algorithm = lincs ; holonomic constraints, GolP has been tested with lincs only constraints = hbonds ; bonds with H-atoms constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs rlist = 1.1 ; short-range neighborlist cutoff (in nm) ; Periodic boundary conditions pbc = xy ; 2-D PBC ; Method for doing Van der Waals vdw-type = switch rvdw-switch = 0.9 rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics rcoulomb = 1.1 ; short-range electrostatic cutoff (in nm) pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT ewald_rtol = 1e-5 ewald_geometry = 3dc ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 optimize_fft = yes ; Temperature coupling is on tcoupl = Nose-Hoover ; Nose-Hoover thermostat tc-grps = Protein_HEM GLD Water_and_ions ; three coupling groups - more accurate tau_t = 0.5 0.5 0.5 ; time constant, in ps ref_t = 300 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; nonuniform scaling of box vectors tau_p = 1.0 1.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, in bar compressibility = 0 4.5e-5 ; isothermal compressibility of water, bar^-1 ;
[gmx-users] emstep unit
Dear gromacs users What is the reason of this point that unit of the emstep (step size)is nm? I think ps (unit of time) is more resonable. If I am wrong, please give me explanation about this point. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] emstep unit
On 9/21/13 1:47 PM, Atila Petrosian wrote: Dear gromacs users What is the reason of this point that unit of the emstep (step size)is nm? I think ps (unit of time) is more resonable. If I am wrong, please give me explanation about this point. Energy minimization is a non-dynamical process; there is no time during EM. Step size is in nm. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] emstep unit
Dear Justin Thanks for your reply. Ok. You are right. There is no time during EM. For example, if I use nstep = 10,000 and emstep = 0.01, what means of Step size in this case, exactly? Please give me more explanation. Best wishes for you. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] No such moleculetype SOL
I am doing this tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html I have set up the randomly placed cyclohexane and water throughout the box. The problem is when i try the command grompp -f em.mdp -c biphase.gro -p cyclohexane.top -o em.tpr it errors telling me No such moleculetype SOL. I know SOL is water, and the .top file does not include any sort of .itp that includes water. I've tried to add #include amber99sb.ff/forcefield.itp with no avail. This is strictly just cyclohexane and water, I am not interested in putting a protein inside of it. Commands used: http://pastebin.com/raw.php?i=RaKNCpi4 Files: http://www.sendspace.com/file/ibwk3l Thank you, the help you guys give is extremely appreciated :) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] No such moleculetype SOL
On Sat, Sep 21, 2013 at 9:06 PM, Jonathan Saboury jsab...@gmail.com wrote: I am doing this tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html I have set up the randomly placed cyclohexane and water throughout the box. The problem is when i try the command grompp -f em.mdp -c biphase.gro -p cyclohexane.top -o em.tpr it errors telling me No such moleculetype SOL. I know SOL is water, and the .top file does not include any sort of .itp that includes water. Have a look at how Justin's tutorial's .top gets access to a water topology. Mark I've tried to add #include amber99sb.ff/forcefield.itp with no avail. This is strictly just cyclohexane and water, I am not interested in putting a protein inside of it. Commands used: http://pastebin.com/raw.php?i=RaKNCpi4 Files: http://www.sendspace.com/file/ibwk3l Thank you, the help you guys give is extremely appreciated :) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] restarting the crashed run
Dear all I would like to know the difference between restarting our crashed runs by 1) first generating next.tpr using tpbconv -extend option then running grompp with this *.tpr file and finally running mdrun but with no cpi option 2) same as 1 but with -cpi option 3) using only mdrun command with cpi option and with previous *.tpr (ie not creating new tpr by tpbconv option) 4) using procedure 3 but with no state.cpt file Secondly, if state.cpt contains all the information to continue the simulation then why the simulation should continue at all without providing these files as in procedure 1 and 4 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] emstep unit
On 9/21/13 2:47 PM, Atila Petrosian wrote: Dear Justin Thanks for your reply. Ok. You are right. There is no time during EM. For example, if I use nstep = 10,000 and emstep = 0.01, what means of Step size in this case, exactly? Please give me more explanation. A quick Google search turns up useful information, and Wikipedia has a decent article. Beyond that, it's a topic covered by just about every molecular modeling textbook out there. -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] restarting the crashed run
On 9/21/13 3:46 PM, Nidhi Katyal wrote: Dear all I would like to know the difference between restarting our crashed runs by 1) first generating next.tpr using tpbconv -extend option then running grompp with this *.tpr file Why would you run grompp? If you're using it as a source of coordinates, you're going to be dealing with the initial state, not the last state of the previous simulation, so that's garbage. If you're restarting a crash, then presumably there is no need at all to invoke tpbconv or grompp. and finally running mdrun but with no cpi option Makes no sense. You're basically obliterating the previous simulation. 2) same as 1 but with -cpi option Still no need for grompp, but if providing -cpi to mdrun, you're resuming from the correct state. 3) using only mdrun command with cpi option and with previous *.tpr (ie not creating new tpr by tpbconv option) This is the correct way to proceed. The run will pick up from the state stored in the .cpt file and proceed with the number of steps originally specified in the .tpr file. 4) using procedure 3 but with no state.cpt file The run should start over. Secondly, if state.cpt contains all the information to continue the simulation then why the simulation should continue at all without providing these files as in procedure 1 and 4 Without a .cpt file, the run starts over from the beginning. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: No such moleculetype SOL
Have a look at how Justin's tutorial's .top gets access to a water topology. Mark Thank you very much for the response Mark! I've looked at his .top and it seems to me that how he included it is by adding #include spc.itp. I've added that line to cyclohexane.top before and after the #include cyclohexane.itp with no success (same error as before). I also saw that he added a force field. Would I need to do this if I am not interested in a protein? I want to avoid using PRODRG because it is online which admins can easy see what I uploaded. I feel much more comfortable using programs on my system (the reason I am using acpype). Thanks again :) - Jonathan Saboury On Sat, Sep 21, 2013 at 12:06 PM, Jonathan Saboury jsab...@gmail.comwrote: I am doing this tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html I have set up the randomly placed cyclohexane and water throughout the box. The problem is when i try the command grompp -f em.mdp -c biphase.gro -p cyclohexane.top -o em.tpr it errors telling me No such moleculetype SOL. I know SOL is water, and the .top file does not include any sort of .itp that includes water. I've tried to add #include amber99sb.ff/forcefield.itp with no avail. This is strictly just cyclohexane and water, I am not interested in putting a protein inside of it. Commands used: http://pastebin.com/raw.php?i=RaKNCpi4 Files: http://www.sendspace.com/file/ibwk3l Thank you, the help you guys give is extremely appreciated :) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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: No such moleculetype SOL
On 9/21/13 5:15 PM, Jonathan Saboury wrote: Have a look at how Justin's tutorial's .top gets access to a water topology. Mark Thank you very much for the response Mark! I've looked at his .top and it seems to me that how he included it is by adding #include spc.itp. I've added that line to cyclohexane.top before and after the #include cyclohexane.itp with no success (same error as before). Then something is wrong with the way you've done it, because the job of spc.itp is to define the [moleculetype] SOL and all its relevant parameters. I also saw that he added a force field. Would I need to do this if I am not interested in a protein? You need a parent force field that defines all the bonded and nonbonded interactions in the system. Whether or not this is one that comes with Gromacs or one you design yourself, you still have to satisfy all of the internal mechanics (see Chapter 5). Whether or not there is a protein is completely irrelevant; force fields do much more than just proteins. I want to avoid using PRODRG because it is online which admins can easy see what I uploaded. I feel much more comfortable using programs on my system (the reason I am using acpype). Well, PRODRG parameters are pretty low-quality anyway, but it's a convenient example for doing a tutorial rather than trying to teach people how to use other external software ;) -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Confuse about trjconv tool
Dear users, I was following Justin's tutorial and in the analysis step trjconv was used to account for any periodicity in the system and then analyses were conducted with the so-called corrected trajectory file. The first question is: does it means that particles might diffuse though one side of the box and doesn't get into the box from the opposite side? If not, why does trjconv have to be used? If so, why could't gromacs maintain the periodicity of all particles' coordinates in the production MD? Finally, Is it necessary to use trjconv to currect the trajectory file every time before you conduct any analysis? Please correct me if something is wrong. Your reply will be highly appreciated. Wishes, Zhikun-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] Confuse about trjconv tool
On 9/21/13 10:28 PM, Caizk wrote: Dear users, I was following Justin's tutorial and in the analysis step trjconv was used to account for any periodicity in the system and then analyses were conducted with the so-called corrected trajectory file. The first thing that is important to note is that the use of the word corrected does not imply that the original trajectory is in any way incorrect. It's just a colloquialism because the trjconv output is easier to visualize and thus seems more correct when pulled up in the visualization software of choice, rather than having a bunch of broken molecules and weird lines drawn all over the place. The first question is: does it means that particles might diffuse though one side of the box and doesn't get into the box from the opposite side? No, that is not the case. Periodicity is always correctly maintained during the run. If not, why does trjconv have to be used? If so, why could't gromacs maintain the periodicity of all particles' coordinates in the production MD? It is a waste of CPU cycles for mdrun to try to fix something during the run that doesn't matter at all to the physics going on. Using trjconv is not compulsory for all processes, but it is important for visualization and certain analyses that require intact coordinates (like RMSD). Finally, Is it necessary to use trjconv to currect the trajectory file every time before you conduct any analysis? As above, it depends on the analysis. Most tools handle PBC elegantly. Some don't. -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
