Re: [gmx-users] Failed tests, need help in troubleshooting
Hi Cameron, I meant any log file from a run with the hardware + software combination. The log file contains hardware and software detection output that is useful in identifying issues. Do the unit tests pass? -- Szilárd On Tue, Apr 23, 2019 at 12:38 PM Cameron Fletcher (CF) < circumf...@disroot.org> wrote: > Hello Szilárd, > > Do you mean log files created in each regression test? > > On 23/04/19 3:43 PM, Szilárd Páll wrote: > > What is the hardware you are running this on? Can you share a log file, > > please? > > -- > > Szilárd > > > > > > On Mon, Apr 22, 2019 at 9:24 AM Cameron Fletcher (CF) < > > circumf...@disroot.org> wrote: > > > >> Hello, > >> > >> I have installed gromacs 2019.1 on CentOS 7.6 . > >> While running regressions tests 2019.1 certain tests are failing with > >> errors. > >> > >> I have attached list of some failed tests. > >> > >> > >> Since I am using gcc compilers and openmpi from openhpc repositories > >> the below command was used for cmake. > >> > >> cmake .. > >> -DCMAKE_C_COMPILER=/opt/ohpc/pub/compiler/gcc/7.3.0/bin/gcc > >> -DCMAKE_CXX_COMPILER=/opt/ohpc/pub/compiler/gcc/7.3.0/bin/c++ > >> -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=on -DGMX_GPU=on -DGMX_USE_OPENCL=on > >> > >> cmake version: 3.13.4 > >> gcc version: 7.3.0 > >> openmpi3 version: 3.1.0 > >> > >> > >> What should I be doing further for more troubleshooting. > >> > >> > >> -- > >> CF > >> > >> -- > >> 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. > > > -- > CF > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Failed tests, need help in troubleshooting
Hello Szilárd, Do you mean log files created in each regression test? On 23/04/19 3:43 PM, Szilárd Páll wrote: > What is the hardware you are running this on? Can you share a log file, > please? > -- > Szilárd > > > On Mon, Apr 22, 2019 at 9:24 AM Cameron Fletcher (CF) < > circumf...@disroot.org> wrote: > >> Hello, >> >> I have installed gromacs 2019.1 on CentOS 7.6 . >> While running regressions tests 2019.1 certain tests are failing with >> errors. >> >> I have attached list of some failed tests. >> >> >> Since I am using gcc compilers and openmpi from openhpc repositories >> the below command was used for cmake. >> >> cmake .. >> -DCMAKE_C_COMPILER=/opt/ohpc/pub/compiler/gcc/7.3.0/bin/gcc >> -DCMAKE_CXX_COMPILER=/opt/ohpc/pub/compiler/gcc/7.3.0/bin/c++ >> -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=on -DGMX_GPU=on -DGMX_USE_OPENCL=on >> >> cmake version: 3.13.4 >> gcc version: 7.3.0 >> openmpi3 version: 3.1.0 >> >> >> What should I be doing further for more troubleshooting. >> >> >> -- >> CF >> >> -- >> 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. -- CF -- 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] Failed tests, need help in troubleshooting
What is the hardware you are running this on? Can you share a log file, please? -- Szilárd On Mon, Apr 22, 2019 at 9:24 AM Cameron Fletcher (CF) < circumf...@disroot.org> wrote: > Hello, > > I have installed gromacs 2019.1 on CentOS 7.6 . > While running regressions tests 2019.1 certain tests are failing with > errors. > > I have attached list of some failed tests. > > > Since I am using gcc compilers and openmpi from openhpc repositories > the below command was used for cmake. > > cmake .. > -DCMAKE_C_COMPILER=/opt/ohpc/pub/compiler/gcc/7.3.0/bin/gcc > -DCMAKE_CXX_COMPILER=/opt/ohpc/pub/compiler/gcc/7.3.0/bin/c++ > -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=on -DGMX_GPU=on -DGMX_USE_OPENCL=on > > cmake version: 3.13.4 > gcc version: 7.3.0 > openmpi3 version: 3.1.0 > > > What should I be doing further for more troubleshooting. > > > -- > CF > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] SASA calculation for one replica in REMD
Check gmx sasa -h It is implemented in Gromacs On Tue, Apr 23, 2019 at 2:37 PM Shan Jayasinghe < shanjayasinghe2...@gmail.com> wrote: > Dear Gromacs Users, > > I did replica exchange molecular dynamics simulation which contains 25 > replicas. Now I want to calculate the solvent accessible surface area of > the surfactant (the first replica in my REMD) I used in my simulation at > 298 K. How can I do that? > > Can anyone help me? > > Thank you. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] SASA calculation for one replica in REMD
Hi, I don't know if sasa calculations are implemented in gromacs. But if you know a little bit of Python you can use MDTraj for that: http://mdtraj.org/latest/examples/solvent-accessible-surface-area.html or also Pymol: https://pymolwiki.org/index.php/Get_Area Cheers, Simone Il mar 23 apr 2019, 11:07 Shan Jayasinghe ha scritto: > Dear Gromacs Users, > > I did replica exchange molecular dynamics simulation which contains 25 > replicas. Now I want to calculate the solvent accessible surface area of > the surfactant (the first replica in my REMD) I used in my simulation at > 298 K. How can I do that? > > Can anyone help me? > > Thank you. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] SASA calculation for one replica in REMD
Dear Gromacs Users, I did replica exchange molecular dynamics simulation which contains 25 replicas. Now I want to calculate the solvent accessible surface area of the surfactant (the first replica in my REMD) I used in my simulation at 298 K. How can I do that? Can anyone help me? Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Removing periodic boundary conditions on a dimer
HI, I actually just did it after posting this post and the two monomers appeared to be good (no separated) but the ligand is on the opposite site and when I tried to center nothing happen. Le mar. 23 avr. 2019 à 10:54, Simone Orioli a écrit : > Hi, > Have you tried the following? It usually worked for me, but I used to run > simulations on old versions of Gromacs so it might be deprecated. > trjconv -f system.xtc -s system.tpr -o system_nojump.xtc -pbc mol > > > Il mar 23 apr 2019, 10:51 Nawel Mele ha scritto: > > > Dear Gromacs users, > > > > I have a dimer system with a ligand in one of the monomer. I am trying to > > remove the periodic boundary conditions to visualise my simulation but > > whatever steps I used the monomers don't want to be centered in the box. > > I tried these steps using a custom index file corresponding to the > residues > > near the active site so I would center around them: > > > > trjconv -f system.xtc -s system.tpr -o system_nojump.xtc -pbc nojump > > trjconv -f system_nojump.xtc -s system.tpr -o system_center.xtc -center > > -pbc whole -ur compact -n index_file_center.ndx > > > > I am confused on the steps I should be using with these kind of system, > do > > you have any suggestions ? > > > > Many thanks, > > > > Regards > > > > -- > > > > Dr Nawel Mele, > > T: +33 (0) 634443794 (Fr) > > > > +44 (0) 7704331840 (UK) > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Dr Nawel Mele, T: +33 (0) 634443794 (Fr) +44 (0) 7704331840 (UK) -- 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] Removing periodic boundary conditions on a dimer
Hi, Have you tried the following? It usually worked for me, but I used to run simulations on old versions of Gromacs so it might be deprecated. trjconv -f system.xtc -s system.tpr -o system_nojump.xtc -pbc mol Il mar 23 apr 2019, 10:51 Nawel Mele ha scritto: > Dear Gromacs users, > > I have a dimer system with a ligand in one of the monomer. I am trying to > remove the periodic boundary conditions to visualise my simulation but > whatever steps I used the monomers don't want to be centered in the box. > I tried these steps using a custom index file corresponding to the residues > near the active site so I would center around them: > > trjconv -f system.xtc -s system.tpr -o system_nojump.xtc -pbc nojump > trjconv -f system_nojump.xtc -s system.tpr -o system_center.xtc -center > -pbc whole -ur compact -n index_file_center.ndx > > I am confused on the steps I should be using with these kind of system, do > you have any suggestions ? > > Many thanks, > > Regards > > -- > > Dr Nawel Mele, > T: +33 (0) 634443794 (Fr) > > +44 (0) 7704331840 (UK) > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Removing periodic boundary conditions on a dimer
Dear Gromacs users, I have a dimer system with a ligand in one of the monomer. I am trying to remove the periodic boundary conditions to visualise my simulation but whatever steps I used the monomers don't want to be centered in the box. I tried these steps using a custom index file corresponding to the residues near the active site so I would center around them: trjconv -f system.xtc -s system.tpr -o system_nojump.xtc -pbc nojump trjconv -f system_nojump.xtc -s system.tpr -o system_center.xtc -center -pbc whole -ur compact -n index_file_center.ndx I am confused on the steps I should be using with these kind of system, do you have any suggestions ? Many thanks, Regards -- Dr Nawel Mele, T: +33 (0) 634443794 (Fr) +44 (0) 7704331840 (UK) -- 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] increase membrane dimensions
thank you John for your help, I solved using gmx genconf and the KALP15 tutorial, charm gui also worked, but I preferred to use gromos ff Emiliano On 2019-04-16 17:48, John Whittaker wrote: Sorry for the double post, but you could also try using CHARMM-GUI. http://www.charmm-gui.org/ That way you don't have to deal with implementing the Berger lipids into the gromos force field (note that CHARMM is all-atom while gromos is united-atom). I have only used it to make a pure lipid bilayer, though, so I'm not sure how easy it is to use to embed a protein in a membrane. The program also generates necessary GROMACS input files for you if you choose. - John -- Dr. Emiliano De Santis, PhD -- 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] Multiple MD simulation
Dear all, I have done the long 200ns MD simulation of protein in water. I have received a comment from the reviewer that for the convergence of the results I have to perform multiple simulations using different initial conformations. Can anyone tell me the criteria for taking the different initial conformations of protein and how to check the convergence of the results? Any help regarding this will be highly appreciated. Thanks in advance Ishrat Jahan Research Scholar Department Of Chemistry A.M.U Aligarh -- 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.
