[gmx-users] conversion of amber outputs to gromacs
Dear gromacs users I did md simulation of my system (protein+ligand) using amber. I want to do some analysis using gromacs. In gromacs, I need to xtc and top file for analysis. How do I convert mdcrd to xtc and prmtop to top files? I used AMBER 10 for doing MD simulation. I used amber03 force field for protein and antechamber for ligand. Any help will highly appreciated. -- 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] extracting velocities
Hi Mah, g_traj -ov or use trjconv to write a .gro/.g96 with velocities. Cheers, Tsjerk On Dec 26, 2014 7:36 AM, mah maz mahma...@gmail.com wrote: Dear all, What are the ways of extracting velocities from output files? I have used g_traj -f traj.trr -s topol.top but couldn't get the velocities. Are there any other commands to help me in this regard? 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. -- 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] extracting velocities
Thank you again Tsjerk! You mean -av all_veloc.xvg? Could you please tell me the differences between -cv veloc.pdb and the mentioned command? Regards ,Mah On Fri, Dec 26, 2014 at 10:05 AM, mah maz mahma...@gmail.com wrote: Dear all, What are the ways of extracting velocities from output files? I have used g_traj -f traj.trr -s topol.top but couldn't get the velocities. Are there any other commands to help me in this regard? 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] extracting velocities
No, I meant -ov It writes the velocities for the selection. Cheers, Tsjerk On Dec 26, 2014 9:54 AM, mah maz mahma...@gmail.com wrote: Thank you again Tsjerk! You mean -av all_veloc.xvg? Could you please tell me the differences between -cv veloc.pdb and the mentioned command? Regards ,Mah On Fri, Dec 26, 2014 at 10:05 AM, mah maz mahma...@gmail.com wrote: Dear all, What are the ways of extracting velocities from output files? I have used g_traj -f traj.trr -s topol.top but couldn't get the velocities. Are there any other commands to help me in this regard? 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. -- 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] MMPBSA GMXPBSA 2.1
Hi Thomas, please forward your request to the GMXPBSA mailing list: https://groups.google.com/forum/#!forum/gmxpbsa probably it is a problem about the configuration Best and On 26/12/2014 08:57, Tom wrote: Dear GXM Users, Is there anyone who has the experience of GMXPBSA 2.1? I download the package and DEMO and gave a quick test of DEMO. There is always a Error report for all the 3 Examples in the DEMO. e.g. for the Example 1 - Setting the PBS queque variables 01:49:50 Generating the centered PDB structures in P53... 01:49:50 ERROR: I could not find _comp0.pdb in /home/user1/Research/Software/DEMO/EXAMPLE1/P53. Exiting... -- Thanks for the help! Thomas -- Andrea Spitaleri PhD D3 - Drug Discovery Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 http://www.iit.it/en/d3-people/andrea-spitaleri.html ORCID: http://orcid.org/-0003-3012-3557 -- 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 use gmx convert-tpr for GMX5.0.4
On Fri, Dec 26, 2014 at 4:33 AM, Smart Eagle wangy...@gmail.com wrote: Hi all, I can use tpbconv to restart or extend simulations for GMX 4.x version. Now I have installed the newest verion of GMX 5.0.4, and I found the tpbconv command had been changed into gmx convert-tpr. But when I use this gmx convert-tpr I got the above error: $ gmx convert-tpr -h -bash: gmx: command not found Just like you needed to do with 4.x, you need to set up your environment to find the installation you've made. bash is telling you that you haven't done that, because it can't find gmx in your PATH environment variable. See http://www.gromacs.org/Documentation/Installation_Instructions#getting-access-to-gromacs-after-installation Mark the information of the GMX I installed is : GROMACS: gmx tpbconv, VERSION 5.0.4 Executable: /lustre/software/gromacs/gromacs-5.0.4/GPU/impi_fftw_sse2/bin/gmx_ mpi Library dir: /lustre/software/gromacs/gromacs-5.0.4/GPU/impi_fftw_sse2/share/gr omacs/top so is there anybody who can give me a suggestion on how to use this new command gmx convert-tpr? Thank you very much! cheers Yukun Wang -- 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.
Re: [gmx-users] gmxcheck : Magic Number Error in XTC file (read 0, should be 1995)
Hi, The most likely explanation is that you were using a network file system that dropped out for some time, was later restored, and it lost some data in the meantime. This might happen if it was caching data before writing it to disk, telling mdrun everything was OK, and something traumatic happened in the meantime. mdrun can't reasonably find out anything until its next attempt to write a file to disk, and whether a file system can, does or should report failure at that time is up for debate. I would make inquiries of your system administrators, and perhaps encourage them to make the file system more robust. You might like to take steps to write your files to real disk that is local to the compute node of MPI rank 0, and transfer the file back at the end of the run. Since you've had problems, you should definitely add a gmxcheck stage to your workflow between restarts. Mark On Thu, Dec 25, 2014 at 10:00 AM, Amit Kumawat amit.kumawa...@gmail.com wrote: Thank you very much David. Out of the complete trajectory I identified all those frames which are corrupted and manually concatenated the rest of the trajectory. Can you provide me suggestion for the possible source of error. Because in the log file I could not see any out of disk space error and I have been using the same version of gromacs for initiating or extending the simulation Regards, Amit R. Kumawat Junior Research Fellow, C/O Dr. Suman Chakrabarty Physical Materials Chemistry Division CSIR-National Chemical Laboratory Pune, India - 411008 Mobile 09579195769 On Wed, Dec 24, 2014 at 8:56 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2014-12-24 15:33, Amit Kumawat wrote: Dear Gromacs Users, I have a trajectory of 2microsecond. I am trying to use gmxcheck to analyse trajectory but I am getting following error; Program gmxcheck, VERSION 4.6.5 Source code file: /home/suman/sources/gromacs-4.6.5/src/gmxlib/xtcio.c, line: 92 Fatal error: Magic Number Error in XTC file (read 0, should be 1995) I have seen similar questions in the mailing list describing the trajectory may be corrupted. If its true in all the cases of this error, Is there any way to recover the trajectory? Please provide suggestion to solve the error. start with trjconv -f old.xtc -o new.xtc to see how much is corrupt. Regards, Amit = Amit R. Kumawat Junior Research Fellow, Physical Materials Chemistry Division CSIR-National Chemical Laboratory Pune, INDIA = -- 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. -- 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] Umbrella sampling along a dihedral angle
Dear Gromacs community, Using enforced rotation potentials I have generated a really smooth rotation of my ligand the catalytic binding domain of my protein. I then put together a simple perl script to calculate the dihedral angle of four particular atoms at each time step using g_angle. Taking a 6 degree interval (for a total of 60 windows to span the 360 degree rotation) I modified the topology with a [ dihedral_restraint ] with the respective dihedral angle for that particular configuation. I plan on then running each window for 10 ns to begin with (according to the PMF profile I can add more time). It is from this point where I am a little stuck. I have gone through a number of posts going back to 2011 with regards to using umbrella sampling along a dihedral angle reaction coordinate. The precise post was from Justin: You'll have to build various configurations that correspond to different dihedral angles (which form the sampling windows), then restrain them. The energy attributed to the restraints is then stored in the .edr file. From these energies, you should be able to construct the energy curve over the sampling windows. There are examples of this in the literature, so I suspect you should be able to find some demonstrations of how it's applied. I was wondering whether gromacs now support this procedure natively? I noticed g_wham has an option -cycl for dihedrals but I am still not sure how this fits in with the traditional gromacs means of generating pull force output as I have only been using distance based rather than angular based umbrella sampling. Many thanks to any insight. Anthony -- 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] extracting velocities
Hi Tsjerk Got the point. It worked; thanks alot! Regards, Mah On Fri, Dec 26, 2014 at 12:23 PM, mah maz mahma...@gmail.com wrote: Thank you again Tsjerk! You mean -av all_veloc.xvg? Could you please tell me the differences between -cv veloc.pdb and the mentioned command? Regards ,Mah On Fri, Dec 26, 2014 at 10:05 AM, mah maz mahma...@gmail.com wrote: Dear all, What are the ways of extracting velocities from output files? I have used g_traj -f traj.trr -s topol.top but couldn't get the velocities. Are there any other commands to help me in this regard? 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.
[gmx-users] How to plot a droplet radius profile as a function of z-direction?
Dear gmx-users,Q1) I would like to plot the radius profile of a water droplet on graphene, as a function of z-direction, as per below:http://journals.aps.org/prl/article/10.1103/PhysRevLett.109.176101/figures/2/largeWhich GROAMCS utility should I use, and how do I go about plotting the profile?Q2) Another question that I have is, suppose I have equilibrated (NVT) a water droplet for 10ns, and would like to plot the H-bond density (along the z-direction),I type the following command:g_density_mpi -f traj_comp.xtc -n system.ndx -s topol.tpr -b 9000 -e 1 -sl 1000 -dens number -o number-density-OH.xvgI was only able to select:SystemGraphene (my substrate)WaterHow can I create a system.ndx such that it allows me to choose the OH (instead of water)?Q3) Regarding Q2, the g_density_mpi utility read the frames contained within the time frame of 9 - 10 ns, but does it average the frames to give a time-averaged density.xvg?Thank you for your time, any feedback is appreciated.Merry Christmas Happy New Year!Regards,Kester -- 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.
