Re: [gmx-users] Installing Extended Genbox
I would generally not try to add it to an existing source repository. Instead, follow one of the suggestions in http://www.gromacs.org/Developer_Zone/Git/Gerrit#How_do_I_get_a_copy_of_my_commit_for_which_someone_else_has_uploaded_a_patch.3f to check out that version. Mark On Tue, Oct 1, 2013 at 6:24 AM, Tegar Nurwahyu Wijaya tnurwahyuwij...@gmail.com wrote: Dear all, I want to install Extended Genbox from gerrit. https://gerrit.gromacs.org/#/c/1175/ How can I put this code into my existing gromacs installation? Thanks. Regards, Tegar -- 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] OPLS/AA + TIP5P, anybody?
Dear Chris, By now 7ns of the MD passed without a single warning. Best Regards, Grzegorz P.s. The mdp: constraints = none integrator = md dt = 0.001; ps nsteps = 1000 ; total 10 ns nstcomm = 1000 nstxout = 0 nstvout = 0 nstfout = 0 nstxtcout = 25 xtc_grps= System nstlog = 1000 nstenergy = 1000 nstlist = 20 ns_type = grid rlist = 1.3 coulombtype = PME fourierspacing = 0.1 pme_order = 4 optimize_fft= yes rcoulomb= 1.3 rvdw= 1.3 vdwtype = cut-off pbc = xyz DispCorr= EnerPres Tcoupl = v-rescale ld_seed = -1 tc-grps = System tau_t = 0.1 ref_t = 300.0 pcoupl = Parrinello-Rahman tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = no cutoff-scheme = Verlet On 2013-09-30 21:47, Christopher Neale wrote: One a system passes EM and a couple of ps of MD, is it always stable indefinitely? If not, then something is wrong somewhere. -- original message -- Dear Chris, I put one tip5p molecule in a center of dodecahedral box - 2nm from that molecule to walls, filled it with tip5p, ran 6000 steps of steep minimization. After another 2704 steps of cg it converged to emtol 1.0. I run 100k steps of nvt on this box afterwards (http://shroom.ibb.waw.pl/tip5p/pure1). But the water is very capricious. If I ran only 2000 steps of steep, the following cg crashed after less than 1000 steps because a water molecule could not be settled. I could not minimize another box, filled only by genbox from an empty gro file (http://shroom.ibb.waw.pl/tip5p/pure2). I understand that you have to have some luck if you run a simulation in pbc with rigid water, which interacts through walls of the box with the other side and was not well placed. Also, I had several segfaults during minimization that I was able to avoid only by limiting the number of cores. I checked distances between OW and LPx on a crashing minimization with a peptide - 2812 water molecules. Maximum force reached 8.8e+24 in 225 steep steps, but all the 5624 distances were rock solid 0.7A, as expected. I still did not post the redmine issue, I want to be sure that I am doing everything correctly. On 2013-09-29 18:47, Christopher Neale wrote: Dear Grzegorz: Under no conditions should any of the tip5p geometry change (for the standard tip5p model). If you find that this is happening, then that is certainly an error. You can check if you like by analyzing your trajectory. However, flexible bonds will allow the distance from the arginine N to the arginine H to vary, which my allow a closer approach of the arginine H to the tip5p dummy site. Did you verify that a water box (no protein) simulates without error? Did you post a redmine issue with .mdp , .gro , and .top files? Chris. -- 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] g_hydorder
Hello everyone, I would like to calculate angle tetrahedral order parameter of water molecules as defined by Chau et al (eq 3). I am using g_hydorder of gromacs 4.6.3 with my index group containing all oxygen atoms of water: g_hydorder -f *.xtc -s *.tpr -o file1.xpm file2.xpm -or file_1.out file_2.out -n index.ndx I am getting following error; No or not correct number (2) of output files :1 It seems from above that correct number should be 2 but user is supplying only 1 and so is the error. But I am giving names of two output files. Also, I am unable to understand what exactly is contained in these two/four output files. I tried to comprehend this by looking at gmx_hydorder.c and could make a guess that I actually need sgmol/sgmean (variables as defined in program) as the final output. Please help me understand the usage of this command in order to fulfill my aim.I have posted this twice but have not got a single reply. Thanks in advance. -- 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] Installing Extended Genbox
Hi Mark, Thank you for your reply. Actually I am not trying to add it to the repository. I have gromacs 4.6 installed in my computer. When I was trying using genbox, an error occurred caused by memory lacking. After searched this mailing list, I got that extended genbox code that can fix my problem. But I don't know how to put that code into my installed gromacs 4.6. Do you or anybody know how to do that? Regards, Tegar On Tue, Oct 1, 2013 at 10:12 AM, Mark Abraham mark.j.abra...@gmail.comwrote: I would generally not try to add it to an existing source repository. Instead, follow one of the suggestions in http://www.gromacs.org/Developer_Zone/Git/Gerrit#How_do_I_get_a_copy_of_my_commit_for_which_someone_else_has_uploaded_a_patch.3f to check out that version. Mark On Tue, Oct 1, 2013 at 6:24 AM, Tegar Nurwahyu Wijaya tnurwahyuwij...@gmail.com wrote: Dear all, I want to install Extended Genbox from gerrit. https://gerrit.gromacs.org/#/c/1175/ How can I put this code into my existing gromacs installation? Thanks. Regards, Tegar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installing Extended Genbox
On 10/1/13 10:58 AM, Tegar Nurwahyu Wijaya wrote: Hi Mark, Thank you for your reply. Actually I am not trying to add it to the repository. I have gromacs 4.6 installed in my computer. When I was trying using genbox, an error occurred caused by memory lacking. After searched this mailing list, I got that extended genbox code that can fix my problem. But I don't know how to put that code into my installed gromacs 4.6. Do you or anybody know how to do that? You need to clone the git repository (i.e. the development code) and then apply the patch with the instructions at the link Mark sent you. Further up on the page is how you get started in terms of obtaining the development code from git. It is unwise to try to apply a patch from the master branch on version 4.6; I doubt it would even work. -Justin Regards, Tegar On Tue, Oct 1, 2013 at 10:12 AM, Mark Abraham mark.j.abra...@gmail.comwrote: I would generally not try to add it to an existing source repository. Instead, follow one of the suggestions in http://www.gromacs.org/Developer_Zone/Git/Gerrit#How_do_I_get_a_copy_of_my_commit_for_which_someone_else_has_uploaded_a_patch.3f to check out that version. Mark On Tue, Oct 1, 2013 at 6:24 AM, Tegar Nurwahyu Wijaya tnurwahyuwij...@gmail.com wrote: Dear all, I want to install Extended Genbox from gerrit. https://gerrit.gromacs.org/#/c/1175/ How can I put this code into my existing gromacs installation? Thanks. Regards, Tegar -- 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 -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installing Extended Genbox
Since that patch is already merged, Tegar can just check out the (default) master branch - see http://www.gromacs.org/Developer_Zone/Git. The CMake build works the same way. I would suggest just using your-build-directory/bin/genbox once you have built it, i.e. do not go to the trouble of installing the development version. You should prefer to use the normal versions of all the tools unless you want to live on the edge! Mark On Tue, Oct 1, 2013 at 5:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/1/13 10:58 AM, Tegar Nurwahyu Wijaya wrote: Hi Mark, Thank you for your reply. Actually I am not trying to add it to the repository. I have gromacs 4.6 installed in my computer. When I was trying using genbox, an error occurred caused by memory lacking. After searched this mailing list, I got that extended genbox code that can fix my problem. But I don't know how to put that code into my installed gromacs 4.6. Do you or anybody know how to do that? You need to clone the git repository (i.e. the development code) and then apply the patch with the instructions at the link Mark sent you. Further up on the page is how you get started in terms of obtaining the development code from git. It is unwise to try to apply a patch from the master branch on version 4.6; I doubt it would even work. -Justin Regards, Tegar On Tue, Oct 1, 2013 at 10:12 AM, Mark Abraham mark.j.abra...@gmail.com* *wrote: I would generally not try to add it to an existing source repository. Instead, follow one of the suggestions in http://www.gromacs.org/**Developer_Zone/Git/Gerrit#How_** do_I_get_a_copy_of_my_commit_**for_which_someone_else_has_** uploaded_a_patch.3fhttp://www.gromacs.org/Developer_Zone/Git/Gerrit#How_do_I_get_a_copy_of_my_commit_for_which_someone_else_has_uploaded_a_patch.3f to check out that version. Mark On Tue, Oct 1, 2013 at 6:24 AM, Tegar Nurwahyu Wijaya tnurwahyuwij...@gmail.com wrote: Dear all, I want to install Extended Genbox from gerrit. https://gerrit.gromacs.org/#/**c/1175/https://gerrit.gromacs.org/#/c/1175/ How can I put this code into my existing gromacs installation? Thanks. Regards, Tegar -- 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-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 -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- 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
[gmx-users] Re: g_hydorder
Please provide me with necessary guidance. I have already posted this thrice but have not got a single reply Thanks in advance. On Tue, Oct 1, 2013 at 3:40 PM, Nidhi Katyal nidhikatyal1...@gmail.comwrote: Hello everyone, I would like to calculate angle tetrahedral order parameter of water molecules as defined by Chau et al (eq 3). I am using g_hydorder of gromacs 4.6.3 with my index group containing all oxygen atoms of water: g_hydorder -f *.xtc -s *.tpr -o file1.xpm file2.xpm -or file_1.out file_2.out -n index.ndx I am getting following error; No or not correct number (2) of output files :1 It seems from above that correct number should be 2 but user is supplying only 1 and so is the error. But I am giving names of two output files. Also, I am unable to understand what exactly is contained in these two/four output files. I tried to comprehend this by looking at gmx_hydorder.c and could make a guess that I actually need sgmol/sgmean (variables as defined in program) as the final output. Please help me understand the usage of this command in order to fulfill my aim.I have posted this twice but have not got a single reply. Thanks in advance. -- 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: g_hydorder
On 2013-10-01 19:51, Nidhi Katyal wrote: Please provide me with necessary guidance. I have already posted this thrice but have not got a single reply Thanks in advance. On Tue, Oct 1, 2013 at 3:40 PM, Nidhi Katyal nidhikatyal1...@gmail.comwrote: Hello everyone, I would like to calculate angle tetrahedral order parameter of water molecules as defined by Chau et al (eq 3). I am using g_hydorder of gromacs 4.6.3 with my index group containing all oxygen atoms of water: g_hydorder -f *.xtc -s *.tpr -o file1.xpm file2.xpm -or file_1.out file_2.out -n index.ndx I am getting following error; No or not correct number (2) of output files :1 Please give exact command line with file names and output cut-and pasted. The program needs indeed two output files of both types. It seems that your command line is ok nevertheless. Please file a redmine issue and assign it to me. It seems from above that correct number should be 2 but user is supplying only 1 and so is the error. But I am giving names of two output files. Also, I am unable to understand what exactly is contained in these two/four output files. I tried to comprehend this by looking at gmx_hydorder.c and could make a guess that I actually need sgmol/sgmean (variables as defined in program) as the final output. Please help me understand the usage of this command in order to fulfill my aim.I have posted this twice but have not got a single reply. Thanks in advance. -- 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 -- 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] ionomer topolgy
On 10/1/13 1:03 PM, Ehsan Sadeghi wrote: Hello, When I use pdb2gmx, the bonds between atoms in the generated conf.gro or conf. pdb file are misplaced. I am using Avogadro for building the atomistic structure, it uses connect command to connect atom correctly. After running pdb2gmx, the generated files do not have connect and they put the bonds is some random places. An suggestion for solving this problem or any other software for building structure without having this problem? The only bonds assigned are what you specify in the .rtp file. If it's not right, fix the .rtp. If I just want to consider bond stretching in my analysis, what should I do to tell gromacs neglect angle,improper, and dihedral? I received 89 errors for not defining them. You'd remove them from the topology entirely. That will be a seriously flawed physical model, unlikely to produce any useful results. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] installing Gromacs4.6.3 with CPMD
Hallo everyone I would like to know if anyone has installed gromacs4.6.3 with CPMD, or how to monitor this installation? I couldn't find the installation procedure in the manual of gromacs4.6 I am looking forwards any suggestions. Thanks Collins -- 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
