[gmx-users] Formatting of spacing in .top and .itp files
Hi, I am running Gromacs 4.5.5. In that rather old version, there is a binary called g_x2top -- I think it is now called something else -- to generate "a primitive topology from a coordinate file." When I use g_x2top with my (custom) force field, g_x2top generates a nicely formatted topology file (either .top or .itp). Here is a snippet from the nicely formatted topology (assuming you display the text in a fixed width font): [ dihedrals ] ; aiajakal functc0c1 c2c3c4c5 8197 113 129 1 11297 113 114 1 11297 113 129 1 82989983 1 829899 115 1 (Only atom indices and a function type are printed because I used the option -noparam in g_x2top.) But, what if I want to generate my own .top or .itp text file, using for example Fortran, Perl, or Python? Are .top and .itp fixed-spaced file formats? In other words, do I have to nicely align the columns as g_x2top does? Or can I just use any number of spaces to delimit the columns, like in the following example? [ dihedrals ] 81 97 113 129 1 112 97 113 114 1 112 97 113 129 1 82 98 99 83 1 82 98 99 115 1 I have tried this ugly formatting, and it seems to give the same results as the nice formatting. But can anyone confirm that .top and .itp are NOT fixed-spaced file formats (unlike .pdb and .gro for example)? Thanks for your time, Andrew DeYoung Carnegie Mellon University -- 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] What is Mnbf/s?
Hi, I feel like this has probably been asked and answered before, but I can't seem to find it. Even if I Google for Mnbf/s, I can't seem to find a definition. In the .log output, what is Mnbf/s? Thanks so much for your time, Andrew DeYoung Carnegie Mellon University -- 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] Pausing and resuming mdrun
Szilard, Thanks for your time; it is really helpful. Just in case people are reading this thread in the future, I want to point out a mistake I made in my original message. I said that using the signal "-SIGSTP" was an alternative to -SIGSTOP. It is actually "-SIGTSTP", not "-SIGSTP". -SIGTSTP is short for "_t_erminal stop," as this reference page explains: http://www.ucs.cam.ac.uk/docs/course-notes/unix-courses/Building/files/signals.pdf Thanks again, Andrew -- 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 can I determine how Gromacs was compiled?
Hi, I'm running Gromacs 4.5.5. Is there a way to determine how Gromacs was compiled on my system? I would like to know whether the person who compiled Gromacs used gcc or icc (both compilers are available and were presumably available when the compilation occurred) and, if possible, what version of FFTW they used. Is there a file or a command that has this information? Thank you so much! Andrew DeYoung Carnegie Mellon University -- 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] Questions about 1-4 interactions in alkanes
Hi, Section 4.2 of the manual has a discussion of dihedrals. The section contains, in part, the following text: With the periodic GROMOS potential a special 1-4 LJ-interaction must be included; with the Ryckaert-Bellemans potential _for alkanes_ the 1-4 interactions must be excluded from the non-bonded list. Note: Ryckaert-Bellemans potentials are also used in e.g. the OPLS force field in combination with 1-4 interactions. You should therefore not modify topologies generated by pdb2gmx in this case. I would like to ask in particular about the statement that with the Ryckaert-Bellemans potential _for alkanes_ the 1-4 interactions must be excluded from the non-bonded list. Here are two questions about that statement: (1) Does that statement apply ONLY to the GROMOS force field, or does it apply to the OPLS-AA force field as well? (2) What is the meaning of alkanes in that statement? - (2a) Does it refer ONLY to saturated hydrocarbons, which contain only hydrogen and carbon and contain only single covalent bonds? (Examples of such molecules are butane, isobutane, pentane, isopentane, and hexane.) - (2b) Or, does it refer to ANY molecule which contains an alkyl group? (An example of such a molecule is the amino acid isoleucine. Isoleucine contains an alkyl group -- isoleucine's side chain is an isopentyl group. Does this mean that I need to EXCLUDE 1-4 interactions among hydrogens and carbons of the isopentyl group from the non-bonded list?) (3) In the OPLS-AA force field, nexcl is usually set to 3, which _initially_ excludes 1-4 interactions. However, in OPLS-AA, 1-4 interactions are explicitly specified in the [ pairs ] section; they are taken at half-strength by setting fudgeQQ = 0.5 and fudgeLJ = 0.5 in the topology. (See, for example, this helpful explanation: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-December/0 77005.html .) If the statement applies to OPLS-AA in addition to GROMOS, and if the statement applies to the alkyl atoms in, e.g. isoleucine, then do I need to EXCLUDE 1-4 interactions among isoleucine's hydrogens and carbons from the [ pairs ] section? Thank you for your time! Andrew DeYoung Carnegie Mellon University -- 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] Embedded view of the users list
Hi, For the past several years and until a few weeks ago, the GMX-Users List webpage here ( http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List ) had an embedded live/interactive view of the list. Messages were organized in threads such that when I clicked on a thread, I could see all posts in the thread on one page. It also had a nice way to search old messages and sort them by date, etc. Could someone please confirm that the embedded live/interactive view of the list has been taken down from http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List ? It is fine if it has been taken down, since I can still browse through the archives here ( https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/ ) and I can search the archives by using google with site:https://mailman-1.sys.kth.se as Mark suggested. But I just wanted to make sure that it is not just me and my browser that no longer sees the embedded live/interactive view of the list. Thank you very much! Andrew DeYoung Carnegie Mellon University -- 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] Specifying the number of OpenMP threads that g_hbond uses
Hi, From the web page http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x , it looks like parallelization for g_hbond (via OpenMP) was added in version 4.6.x. What is a typical command to run g_hbond in parallel? Since I mostly have experience with Gromacs 4.5.5 (which for mdrun has auto MPI threading as the default parallelization, which means I only have to specify the number of threads with -nt), I am not sure how to launch OpenMP for g_hbond in 4.6.x. When I just run g_hbond in 4.6.1 with no extra flags, the output says, Frame loop parallelized with OpenMP using 8 threads. Is there any way to change the number of OpenMP threads that g_hbond uses? Thanks so much! Andrew DeYoung Carnegie Mellon University -- 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] Saving velocities of one atom at every timestep
Hi, I have a rather large system (~10,000 atoms) -- at least, I consider it rather large since I'm using a cluster, not a supercomputer. I want to save the velocities of a single atom of interest at every timestep, so that I can use g_velacc to calculate the velocity autocorrelation function. I only care about the single atom of interest; I'm not interested in the coordinates, velocities, and forces of the other many thousands of atoms in my system. In other words, I have enough disk space to save the velocities of the atom of interest for every timestep for, say, several millions of steps. But I don't have enough space to save the velocities of all 10,000 atoms for every timestep for several millions of steps. I'm running Gromacs version 4.5.5. Setting nstxtcout = 1 allows one to save the coordinates of the groups specified in xtc-grps to the xtc trajectory. Is there any built-in way to save velocities -- rather than coordinates -- for only a specified group (a single atom, in this situation)? Or would it be possible to use the xtc to save the coordinates of the atom of interest at every timestep, and then somehow convert these coordinates to velocities so that I can use g_velacc? I'm using the leapfrog integrator (integrator = md). Thanks so much for your time! Andrew DeYoung Carnegie Mellon University -- 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 can I concatenate multiple g96 configurations into a single trajectory?
Hi, I have been creating several .g96 configuration files by hand (actually, using a scripting language). I like .g96 as a configuration file format because it provides 9 decimal places of precision for the x, y, and z coordinates of the position and velocity of atoms in my system -- whereas .gro and .pdb configuration file formats offer much lower precision. My system is crystalline, and I found many months ago that the lower precision offered by .gro and .pdb is not quite enough to achieve the exact bond lengths that I want in my crystal. Many months ago, Professor van der Spoel suggested on this list that I switch to .g96 for my configurations. So for many months I have been successfully using .g96 configurations as input to grompp to make the .tpr files necessary for simulation. Today, however, I am trying to do something somewhat unusual, and I run into an unusual problem. Suppose I have made three .g96 configurations by hand: conf1.g96, conf2.g96, and conf3.g96. I want to compute the single-point energy of all three configurations. (Why would I want to do this? I have written code in a scripting language to generate frames in which a particular angle is scanned from one extreme to the other; I want to use Gromacs to simply compute the single-point energy at each frame in the scan, without taking any MD moves.) One way to do this might be to run three different zero-step MD simulations, by passing the three configurations separately to grompp, obtaining three separate .tpr files, and passing those three .tpr files to mdrun. But this documentation page http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy warns that zero-step MD simulations have complications related to catering to possible restarts and is not recommended. Doing it that way is also a little inconvenient because eventually I will have dozens or hundreds of separate handmade .g96 configurations for which to calculate the single-point energy, and running hundreds of zero-step simulations would probably require some sort of bash script. So, my thought is to concatenate the three (or more) .g96 configurations into a single trajectory, and then feed that trajectory to the -rerun switch of mdrun to compute the energy of each frame. My question is, how can I concatenate three (or more) .g96 configurations into a single trajectory of any type? I have tried: trjcat -f conf1.g96 conf2.g96 conf3.g96 -o output.trr But I get this error message: --- Program trjcat, VERSION 4.5.5 Source code file: trxio.c, line: 693 Fatal error: Reading trajectories in .g96 format is broken. Please use a different file format. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Reading trajectories in .g96 format may be broken, but reading CONFIGURATIONS in .g96 is not broken, as far as I know (I routinely pass g96 configurations to the -c switch of grompp). Is there any other way I can concatenate three (or more) .g96 configurations into a single trajectory of any type (.trr, .xtc, etc) -- WITHOUT going through .gro or .pdb (e.g., by converting from .g96 using editconf), which have lower precision? Thanks so much for your time! Andrew DeYoung Carnegie Mellon University -- 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 can I concatenate multiple g96 configurations into a single trajectory?
Hi Tsjerk, Thanks so much for your time. Unfortunately, when I tried to convert a .g96 configuration to a .trr trajectory, with this command: trjconv -f conf1.g96 -o conf1.trr I get this error message: --- Program trjconv_d, VERSION 4.5.5 Source code file: trxio.c, line: 693 Fatal error: Reading trajectories in .g96 format is broken. Please use a different file format. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I am running Gromacs 4.5.5. Do you know if there is another way to convert a .g96 configuration to a .trr trajectory, without using trjconv? Or do you know if a different version of Gromacs would not have this problem? Thanks for your time. Andrew DeYoung Carnegie Mellon University -- 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] electrical potential using Gromacs
Hi Fereshte, I used PME. Andrew -Original Message- From: Fereshte Taherian [mailto:tab...@csi.tu-darmstadt.de] Sent: Saturday, January 04, 2014 5:29 PM To: Andrew DeYoung Subject: RE: electrical potential using Gromacs Hi Andrew, Many Thanks for your reply. I am checking my system based on your suggestion. just one additional question, could you please let me know how did you calculate the coulombic interaction in your system, with PME or the other methods? Thanks again, Fereshte Quoting Andrew DeYoung adeyo...@andrew.cmu.edu: Hi, I was able to fix the drift in the electric potential by using particle decomposition parallelization instead of domain decomposition when running the simulations using mdrun (although I still do not know why this fixes the problem). Domain decomposition is the default parallelization in Gromacs, but particle decomposition can be used with the -pd switch of mdrun. However, I think that particle decomposition is slated to be removed in future versions of Gromacs. (I also did not use the -correct switch of g_potential, but that alone did not fix the problem.) Happy New Year. Andrew -Original Message- From: Fereshte Taherian [mailto:tab...@csi.tu-darmstadt.de] Sent: Friday, December 27, 2013 8:04 PM To: adeyo...@andrew.cmu.edu Subject: electrical potential using Gromacs Dear Andrew, I am Fereshte Taherian, and doing my Phd in Technische Universität Darmstadt, Germany. Sorry to bother you. Currently I am using Gromacs to calculate the electrical potential of a ionic liquid confined between two charged surfaces (ewald_geometry = 3dc). Using g_potential I tried to calculate the potential as following: g_potential -correct Looking at the electrical potential, I found a drift in the potential as you mentioned in the Gromacs users forum (http://gromacs.5086.x6.nabble.com/Pseudo-2-D-Ewald-Summation-and-Slab-Geome try-td4880471.html). I really appreciate, if you could let me know how did you fix this problem. Thank you very much. I wish you a happy new year. Best regards, Fereshte -- Fereshte Taherin Tabasi PhD student of Computational Physical Chemistry Center of Smart Interfaces Technische Universität Darmstadt Petersenstraße 32 64287 Darmstadt Tel:(+49)6151-1675040 (Office) Fax:(+49)6151-162048(university) Email: tab...@csi.tu-darmstadt.de http://www.csi.tu-darmstadt.de -- Fereshte Taherin Tabasi PhD student of Computational Physical Chemistry Center of Smart Interfaces Technische Universität Darmstadt Petersenstraße 32 64287 Darmstadt Tel:(+49)6151-1675040 (Office) Fax:(+49)6151-162048(university) Email: tab...@csi.tu-darmstadt.de http://www.csi.tu-darmstadt.de -- 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] What does it mean that particle decomposition does not support checkpointing?
Hi, I am a Gromacs user (I'm running version 4.5.5). I am not _at all_ an experienced programmer, but I was looking through this redmine page about mdrun features to deprecate for 5.0: http://redmine.gromacs.org/issues/1292 Near the top of that page (for issue #1292), it mentions particle decomposition as a feature to deprecate for 5.0: 1) Particle decomposition Doesn't support checkpointing. Doesn't scale because it does not balance load. Removing it will simplify a lot of conditionally executed code paths. The main caveat is whether there are important algorithms whose implementations still require it (see below). What does it mean that particle decomposition doesn't support checkpointing? I use particle decomposition for my Gromacs simulations (in version 4.5.5), and I also save checkpoints from mdrun every 15 minutes using the -cpo flag. The resulting .cpt files seem to work fine -- at least on the surface; I have not checked this in detail -- for doing a restart whenever my system crashes. As a test, I took the final checkpoint file of a run. Then, using the -t flag in mdrun, I started a new simulation using that final checkpoint file. After that new simulation finished, I used trjconv -dump 0 to dump the first frame into a configuration file (in my case, a .g96 file). I compared this to the coordinates in the checkpoint file (as read by gmxdump -cp checkpoint.cpt), and the coordinates in the dumped configuration and in the checkpoint were the same up to the 0.1 nm decimal place (since .g96 files and gmxdump output have different precision). So it seems that, at least in some ways, checkpointing is working even when particle decomposition is used. If so, then what does it mean in the above redmine post that particle decomposition doesn't support checkpointing? If not, why does my very quick, superficial check described in the previous paragraph appear to be successful? Thanks so very much for your time! Andrew DeYoung Carnegie Mellon University -- 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] About g_potential
Hi Guangwei, The simulation box is binned, or sliced, along z in planes parallel to the xy plane. A greater number of slices means the box is sliced finer -- the bins or slices are smaller. The charges are binned (like making a histogram) into those slices, and the potential is calculated by integrating the charge density. So using more slices means more resolution, but using too many slices can lead to irregularities if you haven't saved configurations very often in your trajectory. Andrew DeYoung -- 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] Mailing list archive
Hi, Does anyone know if the gmx-users Archive has been moved or is temporarily down? When I do to: http://lists.gromacs.org/pipermail/gmx-users/ it redirects me to: https://mailman-1.sys.kth.se/pipermail/gmx-users/ but that page says, The requested URL /pipermail/gmx-users/ was not found on this server. Thanks! Andrew DeYoung Carnegie Mellon University -- 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] Mailing list archive
Hi again, I just realized that Mark sent out an email earlier today announcing a power outage for most of the Gromacs infrastructure, starting at midnight. I think it is almost midnight in Stockholm right now, so probably the outage has started and that's why I'm not able to access http://lists.gromacs.org/pipermail/gmx-users/ . Sorry for not noticing this earlier. I will try accessing the archive in a couple of days and will be in touch if I still have trouble. Thanks! Andrew DeYoung Carnegie Mellon University -Original Message- From: Andrew DeYoung Sent: Tuesday, November 26, 2013 4:08 PM To: gmx-us...@gromacs.org Subject: Mailing list archive Hi, Does anyone know if the gmx-users Archive has been moved or is temporarily down? When I do to: http://lists.gromacs.org/pipermail/gmx-users/ it redirects me to: https://mailman-1.sys.kth.se/pipermail/gmx-users/ but that page says, The requested URL /pipermail/gmx-users/ was not found on this server. Thanks! Andrew DeYoung Carnegie Mellon University -- 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.
