Re: [gmx-users] Reduction of system dimensions
So I've removed pbc from the structure and defined new box dims by editconf. Now how I could cut all atoms which are not inclluded to that box ( water in upper and lower leaflets) ? As I told when I did it by means of genbox -cs b2ar_Smaller.gro -box 8.68740 8.41864 9.70145 atom order of the protein have been perturbed. James 2012/12/21 James Starlight jmsstarli...@gmail.com: Hi Tsjerk! 1-Could the hexagonal prism be used with the membrane contained system ? Could you show me visual example of such pbc for bilayer-like systems ? 2-Have GROMACS build-in utilities for such deletion of the atoms within specified cut-offs ( e.g above or below specified distanses) James 2012/12/21 Tsjerk Wassenaar tsje...@gmail.com: Tsjerk -- 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] voltage for membrane?
On Dec 23, 2012, at 11:23 PM, Martin Hoefling martin.hoefl...@gmail.com wrote: You can have a look at http://www.ncbi.nlm.nih.gov/pubmed/21843471 , maybe that does what you want. On http://www.mpibpc.mpg.de/grubmueller/compel you will find installation instructions for the special gromacs version that support the above mentioned protocol. Best, Carsten -- 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] equilibrium state
Dear GROMACS Specialists, We know that one system is at equilibrium state when the variation of Helmholtz or Gibbs free energy be zero. May I ask you say me that how I can understand that my system has reached to equilibrium state in the end of simulation, Please? Best Regards Sara -- 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] about -return of mdrun
On 12/24/12 7:38 AM, Wu Chaofu wrote: Dear gmxers, I want to recalculate potential energies for the frames generated previously. At first, I generate one tpr file with a bit difference from previous one used for generating those frames. Using this tpr file, then I restart mdrun with -return options providing the generated xtc/trr file. However, I find that completely new run is carried out but not based on the previously generated frames. What's wrong with my method? How to reach my aims? Thanks a lot for any reply. Note that 4.5.4 version is employed. The option is -rerun, not -return. Since mdrun does not check for invalid command line arguments, the new run was carried out using the provided .tpr file, as you observed. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] exact average distances with g_mdmat
On 12/23/12 10:03 AM, IsaureCB wrote: Dear gmx-users, I would like to select, for each residue of a model, the residues that are within 3.6 A in average over a simulation. g_mdmat must create this information at some point while generating the contact diagrams, but I would like to extract the real values before they are discretized. I haven't found out how to do this. If sb has any idea or suggestion, it might be very useful. g_dist -dist will print this information. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Regarding coupling constant
On 12/24/12 10:51 AM, sreelakshmi ramesh wrote: Dear all, I am trying repeat a work in which the system is coupled to the Andersen thermostat in which they say they use a coupling constant p = 0.0003 . could anyone of you tell me does it mean tau_t is 0.0003. Any help appreciated See manual section 3.4.8, under the heading Andersen thermostat. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Continuing a simulation
Hi, I am running a protein simulation for 70 ns. I had a MPI run but due to my time constraints on the server, it stopped after 28ns. Now, I want to continue the simulation from the same point up until I use up my server time. I just wanted to confirm that there are two checkpoint files written, md.cpt and md_prev.cpt. It would be really helpful if anyone could advice as to which file would be better to choose to continue the simulation? Also, I wanted a confirmation that if I use: mdrun -s topol.tpr -cpi md.cpt -append Do I also need to add -deffnm md? and if I run mdrun, would it then continue from say 28ns and up until the time specified in the .mdp file? The reason I wanted to confirm this is that before submitting it to the server, I ran it in my local machine and when I see the log file, it shows step 0 and Time 0., does that mean it is starting the simulation from scratch because I had expected it to show me step from wherever it exited last and continue from there on. Would really appreciate if anyone could guide me further. -- Ankita Naithani -- 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: Continuing a simulation plus another error
Hi again, Sorry for the repetition in email. When I ran the mdrun command, I got an error of Attempting to read a checkpoint file of version 13 with code of version 12 Can anyone please help me with this error too? On Mon, Dec 24, 2012 at 4:35 PM, Ankita naithani ankitanaith...@gmail.com wrote: Hi, I am running a protein simulation for 70 ns. I had a MPI run but due to my time constraints on the server, it stopped after 28ns. Now, I want to continue the simulation from the same point up until I use up my server time. I just wanted to confirm that there are two checkpoint files written, md.cpt and md_prev.cpt. It would be really helpful if anyone could advice as to which file would be better to choose to continue the simulation? Also, I wanted a confirmation that if I use: mdrun -s topol.tpr -cpi md.cpt -append Do I also need to add -deffnm md? and if I run mdrun, would it then continue from say 28ns and up until the time specified in the .mdp file? The reason I wanted to confirm this is that before submitting it to the server, I ran it in my local machine and when I see the log file, it shows step 0 and Time 0., does that mean it is starting the simulation from scratch because I had expected it to show me step from wherever it exited last and continue from there on. Would really appreciate if anyone could guide me further. -- Ankita Naithani -- Ankita Naithani -- 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: Continuing a simulation plus another error
On 12/24/12 11:54 AM, Ankita naithani wrote: Hi again, Sorry for the repetition in email. When I ran the mdrun command, I got an error of Attempting to read a checkpoint file of version 13 with code of version 12 Can anyone please help me with this error too? This means you are not using the same version of the code as the previous run. On Mon, Dec 24, 2012 at 4:35 PM, Ankita naithani ankitanaith...@gmail.com wrote: Hi, I am running a protein simulation for 70 ns. I had a MPI run but due to my time constraints on the server, it stopped after 28ns. Now, I want to continue the simulation from the same point up until I use up my server time. I just wanted to confirm that there are two checkpoint files written, md.cpt and md_prev.cpt. It would be really helpful if anyone could advice as to which file would be better to choose to continue the simulation? Checkpoint files are written every 15 minutes by default and the names are recycled between (prefix).cpt and (prefix)_prev.cpt to indicate the most recently saved state and the previous one. Either can be used for continuing the stopped run, but the current state is most advantageous to avoid wasted time. The previous state is saved as a backup in case of a corrupted checkpoint file or frame in the trajectory that would require starting from a previous point. Also, I wanted a confirmation that if I use: mdrun -s topol.tpr -cpi md.cpt -append Do I also need to add -deffnm md? That depends entirely upon the file names present and what the original invocation of mdrun was. and if I run mdrun, would it then continue from say 28ns and up until the time specified in the .mdp file? The reason I wanted to confirm this is that before submitting it to the server, I ran it in my local machine and when I see the log file, it shows step 0 and Time 0., does that mean it is starting the simulation from scratch because I had expected it to show me step from wherever it exited last and continue from there on. The run will start from scratch if for some reason the checkpoint file cannot be found or read for whatever reason. If you are trying to run on a local machine with a different number of processors, for instance, the checkpoint state will not be the same so the run will start over again. Note that most of this information is online for quick reference: http://www.gromacs.org/Documentation/How-tos/Doing_Restarts#Version_4.x -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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: Continuing a simulation plus another error
Hi Justin, Thank you so much for your response. I also noticed that when I type in gmxcheck -f md.cpt to see which version was used, I get the same fatal error of Attempting to read a checkpoint file of version 13 with code of version 12. In my linux machine, the gromacs version is 4.5.5 and the one on the cluster is also 4.5.5. I just offloaded the data from the cluster and was trying to run the test for continuing simulation before submitting it to the cluster for continuation. Could you please suggest me something in this regard too. I understand that the versions would be different but my system and cluster have the same version of gromacs. Also, is version 13 being used by gromacs 4.6? In that case, how do we continue a simulation with that version? If somehow someone updated the software or switched it to gromacs 4.6 in the cluster, I will then directly invoke mdrun there but I would need to know if the command would be the same for continuing the simulation in gromacs 4.6? i.e. mdrun -cpi md.cpt -s md.tpr Sorry for bothering with silly questions, my time on the cluster runs out in 2 days so I really could do with as much help I can for now On Mon, Dec 24, 2012 at 5:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/24/12 11:54 AM, Ankita naithani wrote: Hi again, Sorry for the repetition in email. When I ran the mdrun command, I got an error of Attempting to read a checkpoint file of version 13 with code of version 12 Can anyone please help me with this error too? This means you are not using the same version of the code as the previous run. On Mon, Dec 24, 2012 at 4:35 PM, Ankita naithani ankitanaith...@gmail.com wrote: Hi, I am running a protein simulation for 70 ns. I had a MPI run but due to my time constraints on the server, it stopped after 28ns. Now, I want to continue the simulation from the same point up until I use up my server time. I just wanted to confirm that there are two checkpoint files written, md.cpt and md_prev.cpt. It would be really helpful if anyone could advice as to which file would be better to choose to continue the simulation? Checkpoint files are written every 15 minutes by default and the names are recycled between (prefix).cpt and (prefix)_prev.cpt to indicate the most recently saved state and the previous one. Either can be used for continuing the stopped run, but the current state is most advantageous to avoid wasted time. The previous state is saved as a backup in case of a corrupted checkpoint file or frame in the trajectory that would require starting from a previous point. Also, I wanted a confirmation that if I use: mdrun -s topol.tpr -cpi md.cpt -append Do I also need to add -deffnm md? That depends entirely upon the file names present and what the original invocation of mdrun was. and if I run mdrun, would it then continue from say 28ns and up until the time specified in the .mdp file? The reason I wanted to confirm this is that before submitting it to the server, I ran it in my local machine and when I see the log file, it shows step 0 and Time 0., does that mean it is starting the simulation from scratch because I had expected it to show me step from wherever it exited last and continue from there on. The run will start from scratch if for some reason the checkpoint file cannot be found or read for whatever reason. If you are trying to run on a local machine with a different number of processors, for instance, the checkpoint state will not be the same so the run will start over again. Note that most of this information is online for quick reference: http://www.gromacs.org/Documentation/How-tos/Doing_Restarts#Version_4.x -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- Ankita Naithani -- 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: Continuing a simulation plus another error
On 12/24/12 12:43 PM, Ankita naithani wrote: Hi Justin, Thank you so much for your response. I also noticed that when I type in gmxcheck -f md.cpt to see which version was used, I get the same fatal error of Attempting to read a checkpoint file of version 13 with code of version 12. In my linux machine, the gromacs version is 4.5.5 and the one on the cluster is also 4.5.5. I just offloaded the data from the cluster and was trying to run the test for continuing simulation before submitting it to the cluster for continuation. There is a mismatch somewhere. Run any command simply with the -h flag or read the printed information of any command invocation to see the version. Your executables are newer than the version of Gromacs used to do the original run. Could you please suggest me something in this regard too. I understand that the versions would be different but my system and cluster have the same version of gromacs. Also, is version 13 being used by gromacs 4.6? In that case, how do we continue a simulation with that version? You should use a consistent version throughout. Newer versions should always be backwards compatible, but unless you have a specific reason for upgrading (especially between major releases), I would avoid it. If somehow someone updated the software or switched it to gromacs 4.6 in the cluster, I will then directly invoke mdrun there but I would need to know if the command would be the same for continuing the simulation in gromacs 4.6? i.e. mdrun -cpi md.cpt -s md.tpr The commands haven't changed in this respect. Adding -cpi -append to whatever you ran before is sufficient to continue the simulation if everything else is consistent. Sorry for bothering with silly questions, my time on the cluster runs out in 2 days so I really could do with as much help I can for now You can always install your own version of Gromacs in a location accessible to you, like your home directory, and run using those executables. Silently replacing a version of software and nuking the old one is a great way to upset users, so hopefully the other version is still available somewhere, even if not in the default $PATH. Only your sysadmins know that, though. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Gibbs free energy
Dear GROMACS Users, I work with NPT ensemble. Is the total energy equal to Gibbs free energy? Thanks in advance. Sara -- 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] Gibbs free energy
Obviosuly not. Total energy in MD = total potential energy + total kinetic energy. Read basis of MD. There are specific methods to get free energy which you should aslo read about. Steven On Mon, Dec 24, 2012 at 6:21 PM, mohammad agha mra...@yahoo.com wrote: Dear GROMACS Users, I work with NPT ensemble. Is the total energy equal to Gibbs free energy? Thanks in advance. Sara -- 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] Re: about -return of mdrun
Dear Justin, I am sorry to spell the word. In fact, I had referred to the -return as -rerun. Could you give me some another suggestion? Thank you very much! Chaofu Wu -- View this message in context: http://gromacs.5086.n6.nabble.com/about-return-of-mdrun-tp5004019p5004035.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: about -return of mdrun
mdrun -rerun your-old-trajectory works. Unfortunately you're asking us to guess what you did wrong, without giving us any detail of what you did... that's tricky :-) Mark On Tue, Dec 25, 2012 at 12:09 AM, xiaowu759 xiaowu...@gmail.com wrote: Dear Justin, I am sorry to spell the word. In fact, I had referred to the -return as -rerun. Could you give me some another suggestion? Thank you very much! Chaofu Wu -- View this message in context: http://gromacs.5086.n6.nabble.com/about-return-of-mdrun-tp5004019p5004035.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] Continuing a simulation
Check out http://www.gromacs.org/Documentation/How-tos/Doing_Restarts On Mon, Dec 24, 2012 at 5:35 PM, Ankita naithani ankitanaith...@gmail.comwrote: Hi, I am running a protein simulation for 70 ns. I had a MPI run but due to my time constraints on the server, it stopped after 28ns. Now, I want to continue the simulation from the same point up until I use up my server time. I just wanted to confirm that there are two checkpoint files written, md.cpt and md_prev.cpt. It would be really helpful if anyone could advice as to which file would be better to choose to continue the simulation? Per the above, use gmxcheck and choose for yourself :-) Also, I wanted a confirmation that if I use: mdrun -s topol.tpr -cpi md.cpt -append Do I also need to add -deffnm md? Don't know, depends in part on the behaviour you want to see... Backing up your files and trying it to see is much more efficient than emailing the list :-) and if I run mdrun, would it then continue from say 28ns and up until the time specified in the .mdp file? The reason I wanted to confirm this is that before submitting it to the server, I ran it in my local machine and when I see the log file, it shows step 0 and Time 0., does that mean it is starting the simulation from scratch because I had expected it to show me step from wherever it exited last and continue from there on. That means the restart didn't work, but without looking at the .log file and knowing the command line and contents of the files, nobody can know why. The restart can only start from the configuration in the .cpt or the .tpr, and in general neither of those will be at the point the crash occurred. Mark -- 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] does error estimate given by g_energy considering auto-correlation?
g_analyze -h probably has relevant things to say On Mon, Dec 24, 2012 at 10:56 PM, zifeng li lizife...@gmail.com wrote: Hi, Gromacs users, I'm using Gromacs 4.5.4 and wondering how is the Err.Est given by g_energy calculated? Is it roughly standard deviation/ sqrt N N is the independent part in trajectory? Thanks Merry Chritmas! best Zifeng -- 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] Rerun same trajectory - Pulling
On 12/24/12 5:53 PM, Steven Neumann wrote: Dear Gmx Users, I run pulling simulation of my ligand away from the protein. I produced 1500 frames and run US windows with 0.1 nm spacing. However, I have a gap in histograms - I need to use lower value of nstxtcout to get the proper window where the gap is as the time it goes away is really short. How can I rerun the same trajectory with lower nstxtcout ? I do not want to use grompp as from the same mdp file with pulling simulation I get different trajectories. My mdp (it is continuation after nvt and npt respectively): title = Umbrella pulling simulation define = -DPOSRES_T ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 15; 0.3 ns nstcomm = 10 ; Output parameters nstxout = 0 nstvout = 0 nstxtcout = 100 ; every 1 ps 1500 frames nstenergy = 500 ; Bond parameters constraint_algorithm= lincs constraints = all-bonds continuation= yes ; continuing from NPT ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb= 1.4 rvdw= 1.2 vdwtype = Switch rvdw-switch = 1.0 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc_grps = Protein FE_Water_and_ions ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 298 298 ; reference temperature, one for each group, in K ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = GLU pull_group1 = LIG pull_rate1 = 0.01 ; 0.001 nm per ps = 1 nm per ns pull_k1 = 2000 ; kJ mol^-1 nm^-2 Shall I use rerun option of mdrun? But I wont be able to change frequency of frames. You can't create frames that aren't there, unfortunately. Saving every 0.2 ps is usually vast overkill; if you have a gap in the sampling, you probably need more windows rather than more frames in the existing ones. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Update atom number after cat 2 file.gro
On 12/24/12 10:08 PM, Kieu Thu Nguyen wrote: Dear All, When i merge 2 file.gro by command cat, the atom number have not updated by itself. Are there any method for this problem ? Manual manipulation requires manual updating. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Update atom number after cat 2 file.gro
Sorry, i don't see where is manual for updating. KT On Tue, Dec 25, 2012 at 10:24 AM, Justin Lemkul jalem...@vt.edu wrote: On 12/24/12 10:08 PM, Kieu Thu Nguyen wrote: Dear All, When i merge 2 file.gro by command cat, the atom number have not updated by itself. Are there any method for this problem ? Manual manipulation requires manual updating. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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] Update atom number after cat 2 file.gro
On 12/24/12 10:38 PM, Kieu Thu Nguyen wrote: Sorry, i don't see where is manual for updating. I don't mean the Gromacs manual, I mean manual in the sense that if you modify a coordinate file without using one of the Gromacs tools, then you must manually (i.e. by yourself using some external, non-Gromacs means) update the file. In this case, fire up your favorite text editor and do it yourself. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Update atom number after cat 2 file.gro
I got it. Thank Justin ! On Tue, Dec 25, 2012 at 10:40 AM, Justin Lemkul jalem...@vt.edu wrote: I don't mean the Gromacs manual, I mean manual in the sense that if you modify a coordinate file without using one of the Gromacs tools, then you must manually (i.e. by yourself using some external, non-Gromacs means) update the file. In this case, fire up your favorite text editor and do it yourself. -- 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] Gibbs free energy
Dear Steven, Many thanks from your help. In the manual at the section g_energy has been written that the gromacs calculate the delta G as is follows: Delta G = G(N,p,T) - G idgas(N,p,T) = kT ln eˆ(Upot/kT) But I don't understand why Upot? to calculate of delta S, I know that delta S = (internal energy + P*delta V- delta G)/T but here has been written: Delta S(N,p,T) = S(N,p,T) - S idgas(N,p,T) = (Upot + pV - Delta G)/T. May I ask you to answer me about this and the equation of delta G, Please? Best Regards Sara - Original Message - From: Steven Neumann s.neuman...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, December 25, 2012 2:26 AM Subject: Re: [gmx-users] Gibbs free energy Obviosuly not. Total energy in MD = total potential energy + total kinetic energy. Read basis of MD. There are specific methods to get free energy which you should aslo read about. Steven On Mon, Dec 24, 2012 at 6:21 PM, mohammad agha mra...@yahoo.com wrote: Dear GROMACS Users, I work with NPT ensemble. Is the total energy equal to Gibbs free energy? Thanks in advance. Sara -- 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
[gmx-users] Gibbs free energy
Dear Steven, Many thanks from your help. In the manual at the section g_energy has been written that the gromacs calculate the delta G as is follows: Delta G = G(N,p,T) - G idgas(N,p,T) = kT ln eˆ(Upot/kT) But I don't understand why Upot? to calculate of delta S, I know that delta S = (internal energy + P*delta V- delta G)/T but here has been written: Delta S(N,p,T) = S(N,p,T) - S idgas(N,p,T) = (Upot + pV - Delta G)/T. May I ask you to answer me about this and the equation of delta G, Please? Best Regards Sara -- 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] doubt regarding make_ndx
Dear all, I try to make my residues of interest as an index group using the command make_ndx -f conf.gro -o index.ndx. I have entered my residues as r 15 23 27 30 82 84 125 127 129 140 143 184 187 188 191 194 195 198 201 205 206 208 211 228 236 261 263 273 277 282 283 428 429 432 433 438 441 457 459 463 then I renamed the index file using name 26 tunnel q When I checked back my index file, I found some water molecule atoms also inserted in the tunnel group. What could be the problem? Am I doing in the proper way? Thanks a lot for your valuable time. -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] merge .gro, .top files
But i don't see file gromacs_topology_merger.py in the web Vedat gave me. Tsjerk, can you give me the script for updating the number of atoms ? I searched in google, but i have not found it yet. It's really my stupid question, but i don't know why. Thanks ! Best regards, KT On Tue, Dec 18, 2012 at 6:43 PM, Kieu Thu Nguyen kieuthu2...@gmail.comwrote: thank all so much :-) KT On Tue, Dec 18, 2012 at 4:12 PM, Vedat Durmaz dur...@zib.de wrote: there's also an executable topology merger available written in python called gromacs_topology_merger.py as part of a the software package ZIBMolPy designed for conformational analysis at https://github.com/CMD-at-ZIB/**ZIBMolPyhttps://github.com/CMD-at-ZIB/ZIBMolPy given (in the same directory) a topology file topol.top (argument 1) and two (or more) itp files mol1.itp and mol2.itp included in the top file, the tool writes out a new topology file (argument 2) merging the first two molecules from the include sequence of which itp files are given. note: the number of molecules to be merged should be 1 in the [ molecules ] section. if one of them is meant to appear multiple times in the merged topology, the process needs to be repeated accordingly. vedat Am 18.12.2012 09:38, schrieb Erik Marklund: 18 dec 2012 kl. 09.30 skrev Tsjerk Wassenaar: Hi KT, If you mean concatenating frames in .gro files, you can use trjcat or just cat. If you mean merging the coordinates, it's a wee bit more complicated. Since you also ask for top files, I guess that's the case. Here's a snippet of python code that will do the trick: #!/usr/bin/env python import sys f = [open(i).readlines() for i in sys.argv[1:]] print Merged gro file\n%5d % (sum([len(i) for i in f]) - 3*len(f)) print .join([.join(i[2:-1]) for i in f]), print f[0][-1] For the top files, it is necessary to ensure all the moleculetypes are #included, and that the [ molecules ] listing under [ system ] has the right number and order of the molecules in the merged gro file. There's no tool for that that I know of. In principle you could use grompp for checking that. It would print out a heap of warinngs/notes/errors if structure file and topology don't match. Erik Cheers, Tsjerk On Tue, Dec 18, 2012 at 6:18 AM, Kieu Thu Nguyen kieuthu2...@gmail.com wrote: Dear All, I don't know which tools used to merge 2 files .gro, 2 files .top ? Can i use trjcat ? Thanks ! KT -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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 --**- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/**elflab/index.htmlhttp://www2.icm.uu.se/molbio/elflab/index.html -- 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
[gmx-users] protein membrane system
Hi all, I'm trying to simulate a system of POPC- Protein- Water- Ion following the Justin's tutorial of Kalp15-DPPC. I get the system-solved-ion.gro and run energy minimization. I saw some water molecules in em.gro file, therefore, I erase them and then again save the .gro file as a new one. But when I make a new index file, updated the top file and then go through the NVT simulation, I get this fatal error: Warning: atom name 33908 in topol.top and em.gro does not match (HW2 - HW1) Warning: atom name 33909 in topol.top and em.gro does not match (OW - HW2) Warning: atom name 33910 in topol.top and em.gro does not match (HW1 - OW) (more than 20 non-matching atom names) WARNING 1 [file topol.top, line 57]: 43770 non-matching atom names atom names from topol.top will be used atom names from salem.pdb will be ignored Setting gen_seed to 2957 Velocities were taken from a Maxwell distribution at 310 K --- Program grompp, VERSION 4.5.5 Source code file: /home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/kernel/readir.c, line: 1406 Fatal error: 38 atoms are not part of any of the T-Coupling groups For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Sincerely, Shima -- 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] protein membrane system
Hi all, I'm trying to simulate a system of POPC- Protein- Water- Ion following the Justin's tutorial of Kalp15-DPPC. I get the system-solved-ion.gro and run energy minimization. I saw some water molecules in em.gro file, therefore, I erase them and then again save the .gro file as a new one. But when I make a new index file, updated the top file and then go through the NVT simulation, I get this fatal error: Warning: atom name 33908 in topol.top and em.gro does not match (HW2 - HW1) Warning: atom name 33909 in topol.top and em.gro does not match (OW - HW2) Warning: atom name 33910 in topol.top and em.gro does not match (HW1 - OW) (more than 20 non-matching atom names) WARNING 1 [file topol.top, line 57]: 43770 non-matching atom names atom names from topol.top will be used atom names from em.gro will be ignored Setting gen_seed to 2957 Velocities were taken from a Maxwell distribution at 310 K --- Program grompp, VERSION 4.5.5 Source code file: /home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/kernel/readir.c, line: 1406 Fatal error: 38 atoms are not part of any of the T-Coupling groups For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Sincerely, Shima -- 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
