[gmx-users] msd calculation
Dear All, I want to calculate msd for a group of atoms of my system in different directions (x, y and z). What is the exact difference between -type, -lateral and -ten in g_msd command? which one should I use? Thank you! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] trajectory tools don't work with large .xtc / .trr files
Hi, Rafael is probably on the right track. Using a file system with a limit of 2^32 bytes (=2GB) is just not going to work. One way that might happen is if you used a 32-bit Ubuntu, but that's just a guess. Bottom line - get a real 64-bit file system. Mark On Wed, Feb 11, 2015 at 2:26 PM, Rafael R. Pappalardo raf...@us.es wrote: Just one dumb idea. Your ubuntu is 32 or 64 bits? Rafael Rodríguez Pappalardo Depto. Química Física, Univ. de Sevilla El 11/2/2015, a las 13:57, Wojciech Kopeć 9000...@gmail.com escribió: Dear all, I've been using GROMACS successfully for quite some time on several platforms, although after a recent upgrade my main linux workstation to Ubuntu 14.04 and new installation of latest GROMACS (5.0.4) I noticed very strange behaviour of several tools (mainly trjconv and gmxcheck). Basically when I try to use them on my trajectories, in simplest case trjconv -f traj.xtc I get the error: Source code file /home/wojciech2/GROMACS-5.0.4/gromacs-5.0.4/src/gromacs/fileio/gmxfio.c, line: 513 Can not open file: traj.xtc Needless to say the file exists in the given directory. It happens to all files that I've accumulated over the years (with different GROMACS versions); files themselves are not damaged as they work perfectly on my mac with the same GROMACS version, installed in the same way. Also when I reduced the size (simply using -skip) command of the trajectories on my mac and transferred them to my workstation, the very same tools work without any problems. However, as soon as the file size is above ~2 GB, it throws me the above mentioned error. Any clues? Thanks, Wojciech -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to reply a message?
Dear Gromacs users, How can I reply to a message in user's mail list? I can not find any interface element for that. Best regards, Igor Shchechkin -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to reply a message?
On 2/11/15 3:40 PM, Igor Shchechkin wrote: Dear Gromacs users, How can I reply to a message in user's mail list? I can not find any interface element for that. Reply like any other email you get. The message is sent to the list address, which then propagates to everyone subscribed. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Effect of time step size
On 2/11/15 4:36 AM, Faezeh Pousaneh wrote: Dear Justin, Thank you. You are right about we must check validity of typologies attached in Gromacs webpage, but I just took it for test of influence of 'time step' on results when I was faced with similar problem in my own defined molecule. I initially was simulating my Lutidine molecule, so let me please give details of it, (running time 15 ns with same .mdp file as I sent before except this time both with Parrinello-Rahman, 230 molecules in rectangular box): dt=0.002 Energy Average Err.Est. RMSD Tot-Drift --- Temperature 289.953 0.035.63283 0.189132 (K) Pressure3.707212.6389.728 -0.136095 (bar) Density 956.957 0.678.573773.32218 (kg/m^3) dt=0.001 Energy Average Err.Est. RMSD Tot-Drift --- Temperature 289.994 0.0335.70319 0.0487858 (K) Pressure1.826891.2376.7712.81752 (bar) Density 967.363 0.588.214922.86186 (kg/m^3) Yes, I let time for relaxation and I ignore those times before equilibration. I do determine time-dependence of parameters like density and etc, but also I check RMSD of lutidine-lutidine in order to carefully collect the data which are stable. But as you see still there are difference in densities? Isn't is big difference? Assuming the dt = 0.001 result is more accurate, it's a 1% difference, which is pretty consistent. Perhaps try scaling tau-p as a function of dt so the coupling response is the same. If all of the settings were the same except for dt, this could result in some difference. What is the expected density with these force field parameters, or is it not known? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] special coulombic interaction in 1-3 atoms (bonded atoms)
On Thu, Feb 12, 2015 at 12:09 AM, Ting Zheng zhengting...@gmail.com wrote: Hi all, I have a problem that puzzle me a long time. In my system I define a angle and two bonds between 2-1-3 and 2-1, 2-3 atoms. Generally the coulomb and LJ interaction between 1-3, 1-2, 2-3 atoms was excluded. However, in my position, the potential parameters for these three atoms is quite abnormal since the interaction (only coulombic interactions) in 1-3 atoms was still existed which means I have add this special interaction into my non-bonded list. So my question is that how should I add this special interactions? I am using Amber force field. It seems that the [pairs] items in the top file can make this special interaction come true. But It seems that additional interaction in 1-4 atom could be added via using the [pairs] items. But I am not quite about this. Is there anyone who can do me a favor about this problem? [pairs] are used to add modified 1-4 interactions, but in principle can be used to add anything, such as 1-3 in your case. Secondly, how should I use only coulomb interactions in my system? Set VDW parameters to zero, mdrun will gleefully take advantage of that! Mark Thanks very much Best Regards Ting -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] the issue of calculation of viscosity with NEMD
cs...@mails.jlu.edu.cn Dear gromacs users: I have an issue when I calculate the viscosity with NEMD. Why the value of 1/viscosity obtained by g_energy in GROMACS remains zero when calculating viscosity with NEMD? The mdp file is below: title = production-runcpp = /lib/cppdefine =constraints =integrator = mddt = 0.001 ; ps !nsteps = 8nstcomm = 1nstxout = 100nstvout = 100nstxtcout = 5000nstfout = 0nstlog = 1nstenergy = 100nstlist = 1ns_type = grid; Periodic boundary conditions: xyz or no =pbc = xyzrlist = 1.3rcoulomb = 1.3rvdw = 1.3 ; OPTIONS FOR ELECTROSTATICS AND VDW =; Method for doing electrostatics =coulombtype = PME; Method for doing Van der Waals =;vdw-type = Switch; cut-off lengths =rvdw-switch = 1.3; Apply long range dispersion corrections for Energy and Pressure =DispCorr = EnerPres; Spacing for the PME/PPPM FFT grid =fourierspacing = 0.08; FFT grid size, when a value is 0 fourierspacing will be used =fourier_nx = 0fourier_ny = 0fourier_nz = 0; EWALD/PME/PPPM parameters =pme_order = 6ewald_rtol = 1e-05ewald_geometry = 3depsilon_surface = 0optimize_fft = yes; Nose-Hoover temperature coupling is onTcoupl = berendsentc-grps = PF6 c10tau_t = 0.05 0.05ref_t = 300.00 300.00; Energy monitoringenergygrps = PF6 c10; Pressure coupling is onPcoupl = notau_p = 1.0;Non-equlibrium MDcos_acceleration = 0.06; Generate velocites is on at 300 K. gen_vel = no gen_temp = 300.00gen_seed = 273529-- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] the issue of calculation of viscosity with NEMD
On 2015-02-12 02:10, 陈思言 wrote: cs...@mails.jlu.edu.cn mailto:cs...@mails.jlu.edu.cn Dear gromacs users: I have an issue when I calculate the viscosity with NEMD. Why the value of 1/viscosity obtained by g_energy in GROMACS remains zero when calculating viscosity with NEMD? you mean 0.0? or almost 0? It worked last time I tried it (2003). The mdp file is below: title = production-run cpp = /lib/cpp define = constraints = integrator = md dt = 0.001 ; ps ! nsteps = 8 nstcomm = 1 nstxout = 100 nstvout = 100 nstxtcout = 5000 nstfout = 0 nstlog = 1 nstenergy = 100 nstlist = 1 ns_type = grid ; Periodic boundary conditions: xyz or no = pbc = xyz rlist = 1.3 rcoulomb = 1.3 rvdw = 1.3 ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = PME ; Method for doing Van der Waals = ;vdw-type = Switch ; cut-off lengths = rvdw-switch = 1.3 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.08 ; 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-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = yes ; Nose-Hoover temperature coupling is on Tcoupl = berendsen tc-grps = PF6 c10 tau_t = 0.05 0.05 ref_t = 300.00 300.00 ; Energy monitoring energygrps = PF6 c10 ; Pressure coupling is on Pcoupl = no tau_p = 1.0 ;Non-equlibrium MD cos_acceleration = 0.06 ; Generate velocites is on at 300 K. gen_vel = no gen_temp = 300.00 gen_seed = 273529 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] counting dihedral transitions not working with gmx angle (Mark Abraham)
Here is the line command end the output : (by the way the GROMACS's vertion is 4.6.5 ) g_angle -type dihedral -f 30iso_amber94_323_2-3_pol.xtc -b 7 -od prova -ot t-ptova -oh h-prova -n indicediedri.ndx . Option Filename Type Description -f 30iso_amber94_323_2-3_pol.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt -n indicediedri.ndx InputIndex file -od prova.xvg Output xvgr/xmgr file -ovangaver.xvg Output, Opt. xvgr/xmgr file -ofdihfrac.xvg Output, Opt. xvgr/xmgr file -ott-ptova.xvg Output, Opt! xvgr/xmgr file -ohh-prova.xvg Output, Opt! xvgr/xmgr file -ocdihcorr.xvg Output, Opt. xvgr/xmgr file -or traj.trr Output, Opt. Trajectory in portable xdr format Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint19 Set the nicelevel -b time 7 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -[no]w bool no View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -typeenum dihedral Type of angle to analyse: angle, dihedral, improper or ryckaert-bellemans -[no]all bool no Plot all angles separately in the averages file, in the order of appearance in the index file. -binwidthreal 1 binwidth (degrees) for calculating the distribution -[no]periodic bool yes Print dihedral angles modulo 360 degrees -[no]chandler bool no Use Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather than cosine correlation function. Trans is defined as phi -60 or phi 60. -[no]avercorr bool no Average the correlation functions for the individual angles/dihedrals -acflen int-1 Length of the ACF, default is half the number of frames -[no]normalize bool yes Normalize ACF -P enum 0 Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3 -fitfn enum noneFit function: none, exp, aexp, exp_exp, vac, exp5, exp7, exp9 or erffit -ncskip int0 Skip this many points in the output file of correlation functions -beginfitreal 0 Time where to begin the exponential fit of the correlation function -endfit real -1 Time where to end the exponential fit of the correlation function, -1 is until the end Group 0 ( -CBCACB+CA) has 116 elements Group 1 ( CACB+CA+CB) has 116 elements Group 2 (-CBCACB+CA-) has 232 elements Group 3 ( diedro) has 4 elements Group 4 (diedro2) has 4 elements Select a group: 3 Selected 3: 'diedro' Last frame 1 time 12.000 Found points in the range from 0 to 359 (max 360) angle = -73.7241 angle^2 = 29402 Std. Dev. = 154.812 Order parameter S^2 = 0.973661 The number of frames is 10. thanks Cristi Amariei -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] trajectory tools don't work with large .xtc / .trr files
Dear all, I've been using GROMACS successfully for quite some time on several platforms, although after a recent upgrade my main linux workstation to Ubuntu 14.04 and new installation of latest GROMACS (5.0.4) I noticed very strange behaviour of several tools (mainly trjconv and gmxcheck). Basically when I try to use them on my trajectories, in simplest case trjconv -f traj.xtc I get the error: Source code file /home/wojciech2/GROMACS-5.0.4/gromacs-5.0.4/src/gromacs/fileio/gmxfio.c, line: 513 Can not open file: traj.xtc Needless to say the file exists in the given directory. It happens to all files that I've accumulated over the years (with different GROMACS versions); files themselves are not damaged as they work perfectly on my mac with the same GROMACS version, installed in the same way. Also when I reduced the size (simply using -skip) command of the trajectories on my mac and transferred them to my workstation, the very same tools work without any problems. However, as soon as the file size is above ~2 GB, it throws me the above mentioned error. Any clues? Thanks, Wojciech -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] trajectory tools don't work with large .xtc / .trr files
Just one dumb idea. Your ubuntu is 32 or 64 bits? Rafael Rodríguez Pappalardo Depto. Química Física, Univ. de Sevilla El 11/2/2015, a las 13:57, Wojciech Kopeć 9000...@gmail.com escribió: Dear all, I've been using GROMACS successfully for quite some time on several platforms, although after a recent upgrade my main linux workstation to Ubuntu 14.04 and new installation of latest GROMACS (5.0.4) I noticed very strange behaviour of several tools (mainly trjconv and gmxcheck). Basically when I try to use them on my trajectories, in simplest case trjconv -f traj.xtc I get the error: Source code file /home/wojciech2/GROMACS-5.0.4/gromacs-5.0.4/src/gromacs/fileio/gmxfio.c, line: 513 Can not open file: traj.xtc Needless to say the file exists in the given directory. It happens to all files that I've accumulated over the years (with different GROMACS versions); files themselves are not damaged as they work perfectly on my mac with the same GROMACS version, installed in the same way. Also when I reduced the size (simply using -skip) command of the trajectories on my mac and transferred them to my workstation, the very same tools work without any problems. However, as soon as the file size is above ~2 GB, it throws me the above mentioned error. Any clues? Thanks, Wojciech -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Insertion of a carbon nanotube in a system
Dear users, I am currently working in the direction of adsorption of nucleic acids on the surface of single-wall carbon nanotubes (SWCNT) and I have made a SWCNT with indices (3,3) using the package Tubegen. What I dont know is how to insert it in my system containing nucleic acids, solvent and ions. Is it possible to add the SWCNT just by making the topology by altering the atom types with the help of pdb2gmx and then add it by using -ci -nmol options of the genbox? Can I use packmole to generate the initial structure by putting all the nucleic acis.PDB, SWCNT.PDB and spce.PDB together? I saw a paper where the ssDNA-SWCNT has been modeled by using xleap package of AMBER which I dont know how to use. Is there any other simpler way for the above purpose? I hope I'm not asking for much. Thanks and regards, Soumadwip Ghosh Research Felllow Indian Institute of Technology, Mumbai India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
