Re: [gmx-users] Question about make_ndx and g_angle
Dear Changwoon, why are you using ./make_ndx instead of make_ndx? Did you try to use the command without ./? Regards El jue, 07-11-2013 a las 14:12 -0800, Chang Woon Jang escribió: Dear Users, I am using openSUSE 12.3 and try to use make_ndx and g_angle. When I try the following command, there is an error message. ./make.ndx -f data.pdb ./make_ndx: error while loading shared libraries: libcudart.so.4:cannot open shared object file: No such file or directory Do I need cuda library in order to use make_ndx and g_angle ? Thanks. Best regards, Changwoon Jang -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] extra gro file generation
Dear Sarah, you have to use the trjconv command with the flags -b -e and -sep. For example: trjconv -f xxx.trr -s xxx.tpr -o out.gro -b (initial frame to read in ps) -e (last frame to read in ps) -sep Regards El mar, 05-11-2013 a las 01:04 -0800, sarah k escribió: Dear all, I'm going to perform a molecular dynamics simulation on a protein. As a default the simulation gives one final *.gro file. I need to get a .gro file after each say 500 ps of my simulation, in addition of the final file. How can I do so? Best regards, Sarah Keshavarz -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] cool down problem
Dear all, I'm having some problems during the cool-down process after the NVT. I'm running the NVT process at a T of 500K for 3ns and everything is going well but when I cool down the system blows up. I am running the cool down for 100ps, I tried to run the process for longer time (500 ps) and decrease nstlist option up to 5 but it seems it doesn't work. The EM seems to be fine with very low forces: Potential Energy = -3.1736706e+05 Maximum force = 2.6573439e+01 on atom 105 Norm of force = 3.1027287e-01 The NVT is compiled with the following mdp: define = -DPOSRES ; position restrain the protein and ligand ; Run parameters integrator = md; leap-frog integrator nsteps = 150 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 1 ; save coordinates every 0.2 ps nstvout = 1 ; save velocities every 0.2 ps nstenergy = 1 ; save energies every 0.2 ps nstlog = 1 ; update log file every 0.2 ps energygrps = NAP NA WAT MET SI3 SI- I LI+ LI- ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching vdwtype = cutoff ns_type = grid ; search neighboring grid cells nstlist = 20 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = NAP NA WAT MET SI3 SI- I LI+ LI- ; two coupling groups - more accurate tau_t = 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 ; time constant, in ps ref_t = 500 500 500 500 500 500 500 500 500 ; reference temperature, one for each group, in K ; Pressure coupling pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 298 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed The cooldown mdp is the following: integrator = md tinit= 0 dt = 0.001 nsteps = 10; 100 ps simulation_part = 1 init_step= 0 comm-mode= Linear nstcomm = 1 comm-grps= bd-fric = 0 ld-seed = 1993 rtpi = 0.05 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 500 nstenergy= 100 nstxtcout= 500 xtc-precision= 1000 xtc-grps = nstlist = 10 ns_type = grid pbc = xyz periodic_molecules = no rlist= 0.9 coulombtype = PME rcoulomb-switch = 0 rcoulomb = 0.9 epsilon_r= 1 epsilon_rf = 1 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.0 DispCorr = No table-extension = 1 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 6 ewald_rtol = 1e-5 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = yes gb_algorithm = Still nstgbradii = 1 rgbradii = 2 gb_epsilon_solvent = 80 gb_saltconc = 0 OBC(II) gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 sa_surface_tension = 2.092 Tcoupl = v-rescale tc-grps = system tau_t= 0.1 ref_t= 1000 Pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p= 2 compressibility = 4.5e-5 ref_p= 1 refcoord_scaling = No andersen_seed= 815131 annealing= single annealing_npoints= 2 annealing_time = 0 80 annealing_temp = 500 298 gen_vel = no gen_temp = 500 gen_seed =
Re: [gmx-users] cool down problem
Dear Justin, I ran a short simulation (200ps) with the cool down under NVT and now it seems the system is working. In addition, I removed from the NVT options the tc for all the groups. Thank you, Riccardo El jue, 31-10-2013 a las 08:31 -0400, Justin Lemkul escribió: On 10/31/13 8:25 AM, Riccardo Concu wrote: Dear all, I'm having some problems during the cool-down process after the NVT. I'm running the NVT process at a T of 500K for 3ns and everything is going well but when I cool down the system blows up. I am running the cool down for 100ps, I tried to run the process for longer time (500 ps) and decrease nstlist option up to 5 but it seems it doesn't work. The EM seems to be fine with very low forces: Potential Energy = -3.1736706e+05 Maximum force = 2.6573439e+01 on atom 105 Norm of force = 3.1027287e-01 The NVT is compiled with the following mdp: define = -DPOSRES ; position restrain the protein and ligand ; Run parameters integrator = md; leap-frog integrator nsteps = 150 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 1 ; save coordinates every 0.2 ps nstvout = 1 ; save velocities every 0.2 ps nstenergy = 1 ; save energies every 0.2 ps nstlog = 1 ; update log file every 0.2 ps energygrps = NAP NA WAT MET SI3 SI- I LI+ LI- ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching vdwtype = cutoff ns_type = grid ; search neighboring grid cells nstlist = 20 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = NAP NA WAT MET SI3 SI- I LI+ LI- ; two coupling groups - more accurate Frankly, I'm amazed this was stable. I can't imagine that any system justifies this many individual thermostats. snip Pcoupl = Parrinello-Rahman I doubt that you want to try to use Parrinello-Rahman while simultaneously decreasing the temperature. Even for equilibration runs at stable temperature, P-R is a poor choice. I would suggest trying your cooling under NVT, or if you absolutely need to do it under NPT, use Berendsen instead; it is much more forgiving. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem vwith ethanol-water solution
Dear Ehsan, Did you try to pack your box with packmol? I have a similar system and packmol pack my system quite well and in a random way. Regards, Riccardo -Original Message- From: Ehsan Sadeghi Sent: Thursday, October 31, 2013 7:25 PM To: Discussion list for GROMACS users Subject: [gmx-users] problem vwith ethanol-water solution Hi gmx users, I want to solvate nafion molecules in a 3:1 ethanol water solution. I used genbox with -ci option to add ethanol to water when generating the box, but it did not work. Then, first I solvated the ethanol in water, and then added the nafion to the system, but these 3 molecules each sit a part from each other in the box in the pdb file. Any suggestion? Kind regards, Ehsan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] No group in index file?
Dear Xu, you have to use the make_ndx option if I'm not wrong. The syntax should be make_ndx -f xxx.gro -o index.ndx Cheers, -Original Message- From: Xu Dong Huang Sent: Thursday, October 31, 2013 8:52 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] No group in index file? Dear all, so after I opened angle.ndx file in a text editor, the file appears to be blank. How can I properly make a index file since the command I issued seems to produce a blank index file? Is there something wrong with my input regarding npt.tpr? Thanks for your input, Xu Huang On Oct 31, 2013, at 1:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/31/13 1:36 PM, Xu Dong Huang wrote: Dear all. Since I am interested in finding the average angle, dihedrals in my system, I attempted to use g_angle, but then I realized I need to make index file using mk_angndx, I issued the following: mk_angndx -s npt.tpr -n angle.ndx and then i used g_angle -f not.xtc -n angle.ndx -ov angle.xvg -noperiodic -type angle and then I get the following error: Fatal error: Error: no groups in indexfile How can my index file not have the groups in there? How can I go about fixing this Inspect it with a text editor and/or gmxcheck. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
