[gmx-users] Alchemical transformation position restrains for B state and citing literature for H-RETI
Dear all, I have two questions concerning MD TI free energy calculations for alchemical transfromations: 1) (For some reasons) I want to restrain the backbone of my protein during TI. However, I do not know to correctly generate position restrains for the mutated B-state. If I use the position restrain file, which I generated for the A state, following warning shows up: WARNING 1 [file posre.itp, line 1470]: Some parameters for bonded interaction involving perturbed atoms are specified explicitly in state A, but not B - copying A to B Can I ignore this warning, or do you have any suggestions for me? 2) I am using replica exchange ( -replex in the mdrun) during the free energy thermodynamic integration MD simulation (H-RETI). Can someone tell me the literature I should cite when I apply this? All the best and thank you very much in advance Johannes -- __ *Technische Universität München* *Johannes Hermann, M.Sc.* Lehrstuhl für Bioverfahrenstechnik Boltzmannstr. 15 D-85748 Garching Tel: +49 8928915730 Fax: +49 8928915714 Email: j.herm...@lrz.tum.de http://www.biovt.mw.tum.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] Can not write a pdb file without atom names (concatenating 2 pdb files)
Dear gromacs users, I have 2 trajectory files as pdb format. I want to have only one file using the following command: gmx_mpi trjcat -f 9_ms.pdb 19.pdb -o mix.pdb -settime I encountered with: - Command line: gmx_mpi trjcat -f 9_ms.pdb 19.pdb -o mix.pdb -settime Reading frame 0 time0.000'c15 t= 3.0', 6250 atoms Reading frame 0 time0.000'c15 t= 3.0', 6250 atoms Reading frame 1 time 3.000 Enter the new start time (ps) for each file. There are two special options, both disable sorting: c (continue) - The start time is taken from the end of the previous file. Use it when your continuation run restarts with t=0. l (last) - The time in this file will be changed the same amount as in the previous. Use it when the time in the new run continues from the end of the previous one, since this takes possible overlap into account. File Current start (ps) New start (ps) - 9_ms.pdb0.000 ps 0 19.pdb0.000 ps 900 Summary of files and start times used: FileStart time Time step - 9_ms.pdb0.000 ps3.000 ps 19.pdb 900.000 ps3.000 ps Back Off! I just backed up mix.pdb to ./#mix.pdb.4# Reading frame 0 time0.000 Continue writing frames from 9_ms.pdb t=0 ps, frame=0 --- Program gmx trjcat, VERSION 5.1.3 Source code file: /root/gromacs_source/gromacs-5.1.3/src/gromacs/fileio/trxio.c, line: 557 Fatal error: Can not write a pdb file without atom names For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- How to resolve this issue? Best, 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] x2top and default dihedral type
When generating dihedrals, x2top sets the function to '1'. I recall there was a way to change that (to 3 in my case) and it worked in modified OPLS-AA. I am working with a different FF now and for the life of me cannot recall I changed that in OPLS. I could also be wrong and it just sets it to '3' by default in OPLS, since all dihedrals are of type 3 in that forcefield. At any rate, i get 1 and want 3. Any help? Thanks, Alex -- 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] membrane-protein simulation
Thanks Justin Got it, it's working. On Wed, Aug 2, 2017 at 10:02 AM, Justin Lemkul wrote: > > > On 8/2/17 5:01 AM, Amir Zeb wrote: > >> Hello gmx-user >> >> I want to simulate a membrane protein with more than one chains like A, B, >> C etc. I generated the strong_posre.itp file as Justing has kindly >> explained in his tutorial, and updated the topol.top file by inserting the >> same lines. I also updated the minim.mdp file by inserting STRONG_POSRES. >> Once I tried the minimization of the system before the shrinking step, I >> got the error as below: >> >> Fatal error: >> [ file strong_posre.itp, line 548 ]: >> Atom index (544) in position_restraints out of bounds (1-543). >> This probably means that you have inserted topology section >> "position_restraints" >> in a part belonging to a different molecule than you intended to. >> In that case move the "position_restraints" section to the right molecule. >> For more information and tips for troubleshooting, please check the >> GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> >> >> I tried so many options but could not fix the issue. Please keep in view >> that the same procedure is working well with a single chain of the >> protein. >> Kindly help me how to fix this issue? >> >> > You need to create restraint files for each chain separately and include > them in each [moleculetype] separately, as explained here: > > http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_ > position_restraints_out_of_bounds > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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] AVX related compiler error during build with P100 RHEL7
Hi, Usually this means, like it says, that the linker isn't able to do the required job. I don't know whether the stock RHEL 7.2 linker can, but I imagine that's the issue. Usually using a devtoolset e.g. https://www.softwarecollections.org/en/scls/rhscl/devtoolset-4/ is the way to get a machine with useful tools on it rather than one with "stable" = "old" tools, particularly when you want to use the latest hardware... Mark On Thu, Aug 3, 2017 at 1:28 AM Guyen Gn wrote: > Any update on this one?? > > On Fri, Jul 14, 2017 at 1:30 PM, Guyen Gn wrote: > > > Any ideas on this one? Thanks! > > > > On Mon, Jul 3, 2017 at 9:33 PM, Guyen Gn wrote: > > > >> Still did not work. change xMIC to xCore and log is below (if it was > >> other way around, then originally it must have not worked). > >> Script file is all oneline. > >> > >> -- Performing Test C_xCORE_AVX512_FLAG_WORKS > >> -- Performing Test C_xCORE_AVX512_FLAG_WORKS - Failed > >> -- Performing Test C_mavx512f_mfma_FLAG_WORKS > >> -- Performing Test C_mavx512f_mfma_FLAG_WORKS - Failed > >> -- Performing Test C_mavx512f_FLAG_WORKS > >> -- Performing Test C_mavx512f_FLAG_WORKS - Failed > >> -- Performing Test C_arch_AVX_FLAG_WORKS > >> -- Performing Test C_arch_AVX_FLAG_WORKS - Failed > >> -- Performing Test C_hgnu_FLAG_WORKS > >> -- Performing Test C_hgnu_FLAG_WORKS - Failed > >> -- Performing Test C_FLAG_WORKS > >> -- Performing Test C_FLAG_WORKS - Success > >> -- Performing Test C_COMPILE_WORKS > >> -- Performing Test C_COMPILE_WORKS - Failed > >> -- Compiler flag was valid, but executable did not build - perhaps > update > >> the binutils package > >> -- Performing Test CXX_xCORE_AVX512_FLAG_WORKS > >> -- Performing Test CXX_xCORE_AVX512_FLAG_WORKS - Failed > >> -- Performing Test CXX_mavx512f_mfma_FLAG_WORKS > >> -- Performing Test CXX_mavx512f_mfma_FLAG_WORKS - Failed > >> -- Performing Test CXX_mavx512f_FLAG_WORKS > >> -- Performing Test CXX_mavx512f_FLAG_WORKS - Failed > >> -- Performing Test CXX_arch_AVX_FLAG_WORKS > >> -- Performing Test CXX_arch_AVX_FLAG_WORKS - Failed > >> -- Performing Test CXX_hgnu_FLAG_WORKS > >> -- Performing Test CXX_hgnu_FLAG_WORKS - Failed > >> -- Performing Test CXX_FLAG_WORKS > >> -- Performing Test CXX_FLAG_WORKS - Success > >> -- Performing Test CXX_COMPILE_WORKS > >> -- Performing Test CXX_COMPILE_WORKS - Failed > >> -- Compiler flag was valid, but executable did not build - perhaps > update > >> the binutils package > >> CMake Error at cmake/gmxManageSimd.cmake:92 (message): > >> Found a compiler flag for AVX 512F support, but some other problem > >> exists. > >> Update your assembler and/or linker, e.g. in the binutils package of > >> your > >> distribution. > >> Call Stack (most recent call first): > >> cmake/gmxManageSimd.cmake:314 (gmx_give_fatal_error_when_sim > >> d_support_not_found) > >> CMakeLists.txt:666 (gmx_manage_simd) > >> > >> > >> -- Configuring incomplete, errors occurred! > >> > >> > >> On Mon, Jul 3, 2017 at 2:44 PM, Mark Abraham > >> wrote: > >> > >>> Hi, > >>> > >>> On Mon, Jul 3, 2017 at 10:50 PM Guyen Gn wrote: > >>> > >>> > Sorry for long wait on response, basically i followed the instruction > >>> at > >>> > nvidia website: > >>> > > >>> > http://www.nvidia.com/object/gromacs-installation.html > >>> > > >>> > I instaled GPU driver versoin 369, as well as CUDA, gcc, cmake. After > >>> that > >>> > it tells to run following: > >>> > > >>> > CC=gcc CXX=g++ cmake -DGMX_OPENMP=ON -DGMX_GPU=ON - > >>> > DGPU_DEPLOYMENT_KIT_ROOT_DIR= -DGMX_BUILD_OWN_FFTW=ON - > >>> > DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_BUILD_TYPE=Release - > >>> > DCMAKE_INSTALL_PREFIX= > >>> > > >>> > I tweaked as follows to fit my environment I setup (basically just > >>> > installation source and run directory: > >>> > CC=gcc CXX=g++ cmake /root/gromacs/gromacs-2016 -DGMX_OPENMP=ON > >>> > -DGMX_GPU=ON -DGPU_DEPLOYMENT_KIT_ROOT_DIR=/usr/local/cuda > >>> > -DGMX_BUILD_OWN_FFTW=ON -DGMX_PREFER_STATIC_LIBS=ON > >>> > -DCMAKE_BUILD_TYPE=Release > >>> > -DCMAKE_INSTALL_PREFIX=/root/gromacs/gromacs-2016-run inside build.sh > >>> shell > >>> > script. > >>> > > >>> > This is the full log, I highlighted toward the end section of code > >>> where it > >>> > started to fail. It appears something related to AVX. Thanks., > >>> > > >>> > [root@localhost gromacs-2016]# ./build.sh > >>> > CMake Error: The source directory "/root/gromacs/gromacs-2016/-" does > >>> not > >>> > exist. > >>> > Specify --help for usage, or press the help button on the CMake GUI. > >>> > ./build.sh: line 2: -DGMX_BUILD_OWN_FFTW=ON: command not found > >>> > ./build.sh: line 3: -DCMAKE_BUILD_TYPE=Release: command not found > >>> > > >>> > >>> All the above is because your script needed editing to handle newlines > >>> from > >>> your copy-paste. > >>> > >>> > >>> > [root@localhost gromacs-2016]# nano -w build.sh > >>> > [root@localhost gromacs-2016]# pwd > >>> > /root/gromacs/gromacs-2016 > >>> > [root@localhost gromacs-2016]# mkdir ~/gromacs/gromac
Re: [gmx-users] AVX related compiler error during build with P100 RHEL7
Any update on this one?? On Fri, Jul 14, 2017 at 1:30 PM, Guyen Gn wrote: > Any ideas on this one? Thanks! > > On Mon, Jul 3, 2017 at 9:33 PM, Guyen Gn wrote: > >> Still did not work. change xMIC to xCore and log is below (if it was >> other way around, then originally it must have not worked). >> Script file is all oneline. >> >> -- Performing Test C_xCORE_AVX512_FLAG_WORKS >> -- Performing Test C_xCORE_AVX512_FLAG_WORKS - Failed >> -- Performing Test C_mavx512f_mfma_FLAG_WORKS >> -- Performing Test C_mavx512f_mfma_FLAG_WORKS - Failed >> -- Performing Test C_mavx512f_FLAG_WORKS >> -- Performing Test C_mavx512f_FLAG_WORKS - Failed >> -- Performing Test C_arch_AVX_FLAG_WORKS >> -- Performing Test C_arch_AVX_FLAG_WORKS - Failed >> -- Performing Test C_hgnu_FLAG_WORKS >> -- Performing Test C_hgnu_FLAG_WORKS - Failed >> -- Performing Test C_FLAG_WORKS >> -- Performing Test C_FLAG_WORKS - Success >> -- Performing Test C_COMPILE_WORKS >> -- Performing Test C_COMPILE_WORKS - Failed >> -- Compiler flag was valid, but executable did not build - perhaps update >> the binutils package >> -- Performing Test CXX_xCORE_AVX512_FLAG_WORKS >> -- Performing Test CXX_xCORE_AVX512_FLAG_WORKS - Failed >> -- Performing Test CXX_mavx512f_mfma_FLAG_WORKS >> -- Performing Test CXX_mavx512f_mfma_FLAG_WORKS - Failed >> -- Performing Test CXX_mavx512f_FLAG_WORKS >> -- Performing Test CXX_mavx512f_FLAG_WORKS - Failed >> -- Performing Test CXX_arch_AVX_FLAG_WORKS >> -- Performing Test CXX_arch_AVX_FLAG_WORKS - Failed >> -- Performing Test CXX_hgnu_FLAG_WORKS >> -- Performing Test CXX_hgnu_FLAG_WORKS - Failed >> -- Performing Test CXX_FLAG_WORKS >> -- Performing Test CXX_FLAG_WORKS - Success >> -- Performing Test CXX_COMPILE_WORKS >> -- Performing Test CXX_COMPILE_WORKS - Failed >> -- Compiler flag was valid, but executable did not build - perhaps update >> the binutils package >> CMake Error at cmake/gmxManageSimd.cmake:92 (message): >> Found a compiler flag for AVX 512F support, but some other problem >> exists. >> Update your assembler and/or linker, e.g. in the binutils package of >> your >> distribution. >> Call Stack (most recent call first): >> cmake/gmxManageSimd.cmake:314 (gmx_give_fatal_error_when_sim >> d_support_not_found) >> CMakeLists.txt:666 (gmx_manage_simd) >> >> >> -- Configuring incomplete, errors occurred! >> >> >> On Mon, Jul 3, 2017 at 2:44 PM, Mark Abraham >> wrote: >> >>> Hi, >>> >>> On Mon, Jul 3, 2017 at 10:50 PM Guyen Gn wrote: >>> >>> > Sorry for long wait on response, basically i followed the instruction >>> at >>> > nvidia website: >>> > >>> > http://www.nvidia.com/object/gromacs-installation.html >>> > >>> > I instaled GPU driver versoin 369, as well as CUDA, gcc, cmake. After >>> that >>> > it tells to run following: >>> > >>> > CC=gcc CXX=g++ cmake -DGMX_OPENMP=ON -DGMX_GPU=ON - >>> > DGPU_DEPLOYMENT_KIT_ROOT_DIR= -DGMX_BUILD_OWN_FFTW=ON - >>> > DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_BUILD_TYPE=Release - >>> > DCMAKE_INSTALL_PREFIX= >>> > >>> > I tweaked as follows to fit my environment I setup (basically just >>> > installation source and run directory: >>> > CC=gcc CXX=g++ cmake /root/gromacs/gromacs-2016 -DGMX_OPENMP=ON >>> > -DGMX_GPU=ON -DGPU_DEPLOYMENT_KIT_ROOT_DIR=/usr/local/cuda >>> > -DGMX_BUILD_OWN_FFTW=ON -DGMX_PREFER_STATIC_LIBS=ON >>> > -DCMAKE_BUILD_TYPE=Release >>> > -DCMAKE_INSTALL_PREFIX=/root/gromacs/gromacs-2016-run inside build.sh >>> shell >>> > script. >>> > >>> > This is the full log, I highlighted toward the end section of code >>> where it >>> > started to fail. It appears something related to AVX. Thanks., >>> > >>> > [root@localhost gromacs-2016]# ./build.sh >>> > CMake Error: The source directory "/root/gromacs/gromacs-2016/-" does >>> not >>> > exist. >>> > Specify --help for usage, or press the help button on the CMake GUI. >>> > ./build.sh: line 2: -DGMX_BUILD_OWN_FFTW=ON: command not found >>> > ./build.sh: line 3: -DCMAKE_BUILD_TYPE=Release: command not found >>> > >>> >>> All the above is because your script needed editing to handle newlines >>> from >>> your copy-paste. >>> >>> >>> > [root@localhost gromacs-2016]# nano -w build.sh >>> > [root@localhost gromacs-2016]# pwd >>> > /root/gromacs/gromacs-2016 >>> > [root@localhost gromacs-2016]# mkdir ~/gromacs/gromacs-run >>> > [root@localhost gromacs-2016]# ./build.sh >>> > -- The C compiler identification is GNU 4.8.5 >>> > -- The CXX compiler identification is GNU 4.8.5 >>> > -- Check for working C compiler: /usr/bin/gcc >>> > -- Check for working C compiler: /usr/bin/gcc -- works >>> > -- Detecting C compiler ABI info >>> > -- Detecting C compiler ABI info - done >>> > -- Check for working CXX compiler: /usr/bin/g++ >>> > -- Check for working CXX compiler: /usr/bin/g++ -- works >>> > -- Detecting CXX compiler ABI info >>> > -- Detecting CXX compiler ABI info - done >>> > -- Performing Test CXXFLAG_STD_CXX0X >>> > -- Performing Test CXXFLAG_STD_CXX0X - Success >>> > -- Performing Test CXX11_SUPPORTED >>> > -
Re: [gmx-users] CHARMM36 for GMX
That's true, a lot of redundant stuff there and once again these are very basic forcefield facts for what biochem folks do. In my case, I have a bunch of very simple situations in crystal structures, but now I gotta use CHARMM or AMBER (lipids!) and charge assignment (half the time perfectly applicable to organic chemistry, yet entirely untouched in this field) in those simple situations becomes a challenge, especially when they control critical physics in the system. All in all, I hate reading detailed FF documentation. However, so as not to post questions like a good 90% of what we see on this board, I'm pretty sure I'll have to with CHARMM. I will do my best not to contribute to the whole "please do my job for me" effort here. :) As I told Mark, it is the developers' fault -- people use the incorrect tool just because it is a great piece of software. Take it as a compliment. As always, thanks. Alex On Wed, Aug 2, 2017 at 12:59 PM, Justin Lemkul wrote: > > > On 8/2/17 2:52 PM, Alex wrote: > >> Yeah, those are indeed there for the particular molecules, thanks. I >> understand that this is the only way to go, it's just that my use of GMX >> is >> somewhat different in that I rarely use molecules in the normal sense, and >> OPLS-AA, being a LEGO for simple groups, has been very convenient with >> that >> catalog you mentioned. Like, place a carboxyl termination somewhere, or >> have a hole in a bulk sheet of graphene, etc. >> >> > All additive force fields are constructed in the same way, from building > blocks. It's just that OPLS-AA uses a huge amount of (redundant in many > cases) atom types and can be mapped to different charges based on different > situations. It's also why OPLS-AA has separate bonded and nonbonded atom > types. There is greater diversity among nonbonded types but fewer bonded > types, reducing the dimensionality of the internal parameters rather than > having huge amounts of duplicated bonded parameters for types that really > aren't different. > > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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] segmentation fault for unknown reason
Hello! I am trying to minimize a periodic MnO2 surface using UFF force fields. I have previously computed many structures using MnO2 clusters. I did not face much problem. However, when I am trying to compute the minimization using the following minim.mdp there is segmentation error as follows. ; minim.mdp - used as input into grompp to generate em.tpr integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 50; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; Short-range electrostatic cut-off rvdw= 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) Error: Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Step=0, Dmax= 1.0e-02 nm, Epot= 3.46301e+34 Fmax= 2.91045e+06, atom= 289 [fen2.hpcc.rutgers.edu:mpi_rank_0][error_sighandler] Caught error: Segmentation fault (signal 11) ./script: line 5: 54036 Segmentation fault (core dumped) gmx_mpi mdrun -ntomp 1 -v -deffnm em I do not understand this problem. Is there anything wrong with my structure or the minim.mdp? *Thank you* *Gangotri Dey* -- 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] CHARMM36 for GMX
On 8/2/17 2:52 PM, Alex wrote: Yeah, those are indeed there for the particular molecules, thanks. I understand that this is the only way to go, it's just that my use of GMX is somewhat different in that I rarely use molecules in the normal sense, and OPLS-AA, being a LEGO for simple groups, has been very convenient with that catalog you mentioned. Like, place a carboxyl termination somewhere, or have a hole in a bulk sheet of graphene, etc. All additive force fields are constructed in the same way, from building blocks. It's just that OPLS-AA uses a huge amount of (redundant in many cases) atom types and can be mapped to different charges based on different situations. It's also why OPLS-AA has separate bonded and nonbonded atom types. There is greater diversity among nonbonded types but fewer bonded types, reducing the dimensionality of the internal parameters rather than having huge amounts of duplicated bonded parameters for types that really aren't different. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] CHARMM36 for GMX
Yeah, those are indeed there for the particular molecules, thanks. I understand that this is the only way to go, it's just that my use of GMX is somewhat different in that I rarely use molecules in the normal sense, and OPLS-AA, being a LEGO for simple groups, has been very convenient with that catalog you mentioned. Like, place a carboxyl termination somewhere, or have a hole in a bulk sheet of graphene, etc. In any case, thank you. Alex On Wed, Aug 2, 2017 at 12:41 PM, Justin Lemkul wrote: > > > On 8/2/17 2:38 PM, Alex wrote: > >> Huh. Most of my work has been with OPLS-AA, so I took that for granted. >> Where would the actual charges be, then? >> >> > In the .rtp file, where residues are defined. Charges are not (and should > not) necessarily be linked to atom types; they are a function of > parametrized groups or molecules. > > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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] CHARMM36 for GMX
On 8/2/17 2:38 PM, Alex wrote: Huh. Most of my work has been with OPLS-AA, so I took that for granted. Where would the actual charges be, then? In the .rtp file, where residues are defined. Charges are not (and should not) necessarily be linked to atom types; they are a function of parametrized groups or molecules. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] CHARMM36 for GMX
Huh. Most of my work has been with OPLS-AA, so I took that for granted. Where would the actual charges be, then? Alex On Wed, Aug 2, 2017 at 12:32 PM, Justin Lemkul wrote: > > > On 8/2/17 2:18 PM, Alex wrote: > >> Hi all, >> >> I am not entirely sure it's a question for the Gromacs community, as this >> is regarding CHARMM36, but it appears that the original forcefield is >> fine, >> while I am confused by its Gromacs version. >> >> Namely this: the MacKerell website distributes a Gromacs version of >> CHARMM36 where ffnonbonded.itp has pretty much all default charges set to >> zero. Is this called for?? >> >> I apologize in advance if this is a dumb or misdirected question, as I've >> never worked with CHARMM before. >> >> > Charges in ffnonbonded.itp are never used by any force field. It's > nothing to do with CHARMM, just a relic of old GROMACS formats and likely a > desire to catalog "default" charges for certain groups. But they serve no > functional purpose. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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] CHARMM36 for GMX
On 8/2/17 2:18 PM, Alex wrote: Hi all, I am not entirely sure it's a question for the Gromacs community, as this is regarding CHARMM36, but it appears that the original forcefield is fine, while I am confused by its Gromacs version. Namely this: the MacKerell website distributes a Gromacs version of CHARMM36 where ffnonbonded.itp has pretty much all default charges set to zero. Is this called for?? I apologize in advance if this is a dumb or misdirected question, as I've never worked with CHARMM before. Charges in ffnonbonded.itp are never used by any force field. It's nothing to do with CHARMM, just a relic of old GROMACS formats and likely a desire to catalog "default" charges for certain groups. But they serve no functional purpose. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] CHARMM36 for GMX
Hi all, I am not entirely sure it's a question for the Gromacs community, as this is regarding CHARMM36, but it appears that the original forcefield is fine, while I am confused by its Gromacs version. Namely this: the MacKerell website distributes a Gromacs version of CHARMM36 where ffnonbonded.itp has pretty much all default charges set to zero. Is this called for?? I apologize in advance if this is a dumb or misdirected question, as I've never worked with CHARMM before. Thank you, Alex -- 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] G_MMPBSA
Did you try the pre-compiled version from here: http://rashmikumari.github.io/g_mmpbsa/Download-and-Installation.html it worked just fine with me on debian and CentOS. Offcourse you need to have APBS installed. On Thu, Jul 27, 2017 at 7:04 PM, Mark Abraham wrote: > Hi, > > You should start by reading and following the installation guide of this > non-GROMACS tool. If you have questions, asking on its forum is probably > best ;-) And please do provide some detail and what you did and where it > went wrong. > > Mark > > On Thu, 27 Jul 2017 18:14 S M Bargeen Turzo > wrote: > > > Hi all, > > > > I am trying to install g_mmpbsa gromacs package( > > http://rashmikumari.github.io/g_mmpbsa/) but it's not working. Can > anyone > > please guide me through the installation process of this package? > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] QM/MM in Gromacs-5.1.4?
Follow the instructions at http://wwwuser.gwdg.de/~ggroenh/qmmm.html Also, you need to set the following variable at compile time -DGMX_QMMM_ORCA=ON -- Clinton King Graduate Student Chemistry Department Brigham Young University > Message: 3 > Date: Wed, 2 Aug 2017 15:01:29 +0200 > From: Albert > To: gmx-us...@gromacs.org > Subject: [gmx-users] QM/MM in Gromacs-5.1.4? > Message-ID: <798bdbd3-6055-79fa-46aa-361cbe067...@gmail.com> > Content-Type: text/plain; charset=utf-8; format=flowed > > Hello, > > I would like to use ORCA as a QM engine for Gromacs QM/MM simulation. I > am just wondering shall we add additional options to cmake when we > compile Gromacs? > > Thanks a lot > > Albert > > > > > -- 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] -multidir option in REMD (GROMACS v2016.1) -resolved
THank you Mark and Johannes,
I finally resolved my problem by using your solutions and can launch my REMD
simulations
Best
Stéphane
--
Message: 1
Date: Wed, 02 Aug 2017 10:59:10 +
From: Mark Abraham
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] -multidir option in REMD (GROMACS v2016.1)
Message-ID:
Content-Type: text/plain; charset="UTF-8"
Hi,
On Wed, Aug 2, 2017 at 11:22 AM ABEL Stephane wrote:
> Dear all,
>
> I would like to do a REMD of a system with 75 replicas (with 75
> directories named md_0,..., md_75) and I have two questions.
>
> 1) To launch the md calculation we should use the followng command :
>
> mpirun -np 4 mdrun_mpi -v -multidir sim[0123] -replex XXX
>
> My question is since I have 75 replicas (directories). How I should set
> the argument of -multidir ? Like this : -multidir md_[01234...75] or only
> "md_".
>
The -multidir option needs a list of all your directories. The best way to
do that is with shell (e.g. wildcard) expansion. Just using "md_" doesn't
get expanded by anything. I recently observed someone suggest that
"md_{0..75}" might do what you want, but I've never tried it. Anyway, md_*
will expand them all, and IIRC mdrun will sort out the ordering from the
values of the REMD control parameter.
> I have used the following command : mdrun_mpi -v -multidir
> ./"$Stage1_FileName"/md_ -replex 500, but the program stops with the
> following error : Need at least two replicas for replica exchange (option
> -multi)
>
Since there's only one directory named, because the shell couldn't expand
anything for you, mdrun doesn't know how to proceed. Pro tip - get it
working for a small number of replicas (e.g. 2) before worrying about using
all 75.
> 2) Second question It is not clear to me how I should set the number of
> step in the mdp file of each replica use in the production runs. For
> instance I want to do a simulation of 50 ns, should I set nsteps =
> 500/75
>
Each simulation is independent and every e.g. mdp parameter is particular
to it. So choose your number of steps in each mdp file to be the length of
a single replica. Obviously nsteps * dt = time in the usual way, but since
we don't know dt, you'll have to compute your nsteps ;-)
Mark
Could you help me ?
--
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Re: [gmx-users] Clayff forcefield
On 8/2/17 5:20 AM, G R wrote: I try to implement CLYFF in gromacs. I created ffbonded.itp, ffnonbonded.itp, atomtype.atp, forcefield.doc, forcefield.itp and molecule.rtp. I want to simulate Kaolinite, and I try to use pdb2gmx to create a topology. My first question is that should I create any other files? second, In molecule.rtp, I just write the atom type, atom name and charges. should I add bonds for each atom? Also, in rtp file, I don't know what should I write as a residue? For a system like you're dealing with, pdb2gmx is not the correct approach. Try x2top with a suitable .n2t file (which you'll have to create). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] LINCS warning during energy minimization of nitrogen with virtual site
On 8/2/17 9:12 AM, Ali Ahmed wrote: Dear all, Thank you for helping me. All I get from grompp is this -- gmx grompp -f grompp.mdp -c N2_box.gro -po mdout.mdp -p topol.top -o topol.tpr Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# NOTE 1 [file grompp.mdp]: The group cutoff scheme is deprecated since GROMACS 5.0 and will be removed in a future release when all interaction forms are supported for the verlet scheme. The verlet scheme already scales better, and it is compatible with GPUs and other accelerators. Setting the LD random seed to 1000542586 Generated 120 of the 120 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 120 of the 120 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'N_2' Cleaning up constraints and constant bonded interactions with virtual sites Analysing residue names: There are: 2493 Other residues Simplify your system - work with one molecule and print out the forces at each step to see if there is something haywire going on. -Justin Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group System is 12462.00 NOTE 2 [file grompp.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. Largest charge group radii for Van der Waals: 0.056, 0.056 nm Largest charge group radii for Coulomb: 0.056, 0.056 nm This run will generate roughly 90 Mb of data There were 2 notes Back Off! I just backed up topol.tpr to ./#topol.tpr.1# gcq#454: "I never see what has been done; I only see what remains to be done." (Marie Curie) On Tue, Aug 1, 2017 at 5:08 PM, Justin Lemkul wrote: On 8/1/17 6:07 PM, Ali Ahmed wrote: Dear Dr. Dallas, Thank you for your reply. Actually, I'm new to GROMACS and I appreciate your support. -- Here is what I get before crashing. Too many warning then crush. This is not diagnostic of anything useful. You've been asked several times to provide the output of grompp, not mdrun. The grompp output can be suggestive of issues you may not have considered. -Justin Step 37, time 0.037 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.002768, max 0.195102 (between atoms 34930 and 34931) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 193194 51.70.1100 0.1100 0.1100 54409 54410 32.30.1100 0.1100 0.1100 On Tue, Aug 1, 2017 at 4:49 PM, Dallas Warren wrote: Copy the output from both of those commands, most importantly (as Mark has asked) that from the first one gmx grompp You need to show people exactly what you are seeing, not what you say you are seeing. The latter you are filtering it, and most likely not providing all the important information. The former allows those trying to help to see all the information that they need to see. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On 2 August 2017 at 04:05, Ali Ahmed wrote: Hi, Thank you for your help. well I used this command gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr gmx mdrun -v -deffnm em and I got all the warnings. Here is my em.mdp - integrator = steep emtol = 10.0 emstep = 0.001 nsteps = 5 energygrps = system ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 cutoff-scheme = group ns_type= grid coulombtype= PME rcoulomb = 1.0 rvdw= 1.0 pbc = xyz On Tue, Aug 1, 2017 at 11:07 AM, Mark Abraham wrote: Hi, No, only mdrun issues LINCS warnings. grompp issues different warnings, and I would like you to check whether you had any from grompp that you may not have considered. :-) Mark On Tue, Aug 1, 2017 at 5:04 PM Ali Ahmed wrote: Dear Mark Yes, all the warnings are from grompp. I have no idea where is the problem in the structure or the topology Thank you On Mon, Jul 31, 2017 at 2:34 PM, Mark Abraham < mark.j.abra...@gmail.com> wrote: Hi, Did you get any warnings from grompp? Mark On Mon, Jul
Re: [gmx-users] Error in itp file
On 8/2/17 12:35 PM, Souvik Dey wrote: Hi, I just generated an itp file from ACPYPE. However, if I try to add ions it shows the following error: Fatal error: Syntax error - File FAD.itp, line 3 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes Can somebody say how do I fix this? This exact situation is described here: http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] pulling of a molecule through protein-membrane system
On 8/2/17 1:16 AM, Alex Mathew wrote: Dear Justin, Well, Charmm-gui not providing an option to make a long box in one direction. So is it fine increasing the box and adding the water in Charmm-gui output pdb file and proceed? Yes. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] membrane-protein simulation
On 8/2/17 5:01 AM, Amir Zeb wrote: Hello gmx-user I want to simulate a membrane protein with more than one chains like A, B, C etc. I generated the strong_posre.itp file as Justing has kindly explained in his tutorial, and updated the topol.top file by inserting the same lines. I also updated the minim.mdp file by inserting STRONG_POSRES. Once I tried the minimization of the system before the shrinking step, I got the error as below: Fatal error: [ file strong_posre.itp, line 548 ]: Atom index (544) in position_restraints out of bounds (1-543). This probably means that you have inserted topology section "position_restraints" in a part belonging to a different molecule than you intended to. In that case move the "position_restraints" section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I tried so many options but could not fix the issue. Please keep in view that the same procedure is working well with a single chain of the protein. Kindly help me how to fix this issue? You need to create restraint files for each chain separately and include them in each [moleculetype] separately, as explained here: http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Creating Custom .rtp files
On 8/2/17 5:07 AM, Momin Ahmad wrote: I think the reason for the weird log is the "|&tee" command that lets you write the output of another command into a file. In the case of the error i could choose the forcefield before the error occurred. The methane was called "CH4" before, i just changed the names for troubleshooting. This time i did copy&paste manually. Files are attached. There are two comments that show the differences in the versions. Again: the two .rtp files for both versions are identical and the same .pdb file is used. Works fine for me using the files you provided on Redmine. I suspect you're just not managing your files correctly. Make sure your methane.rtp is in the force field subdirectory, not the working directory or anywhere else. -Justin Am 01.08.2017 um 20:42 schrieb Justin Lemkul: On 8/1/17 10:32 AM, Momin Ahmad wrote: please finde the files attached to this email: log-files for the 5.1.2 version and the 2016.3 version, also again the .rtp file and the .pdb file The screen output seems garbled to me, with the fatal error coming before the force field selection, and multiple locations being used. I can't figure out what's going on. Your .rtp needs to be in the force field directory that you choose, either locally (within the working directory) or system-wide (wherever that is installed). Note also that "CH4" and "CH41" are different, because one error indicates that pdb2gmx finds CH4 when your .rtp is clearly CH41. -Justin Am 01.08.2017 um 00:48 schrieb Justin Lemkul: On 7/31/17 7:47 AM, Momin Ahmad wrote: Hello, the .rtp file is located in the same directory as the force-field. When i type gmx gmx2pdb . then the log shows that the right path is considered and loads the needed .rtp fiels that already exist in the forc-field file. But my custom one is ignored. Please post the full screen output of pdb2gmx, including the force field selection. If your .rtp file is not being read, it is likely misformatted, in which case you should either write your new residue entries in an existing file or upload it to a file-sharing service so we can provide feedback. -Justin Greets Momin Ahmad Am 25.07.2017 um 16:34 schrieb RAHUL SURESH: On Tue, 25 Jul 2017 at 5:58 PM, Momin Ahmad wrote: Hi, I created a custom .pdb file and the associated .rtp file for the force-field (amber99sb-ildn.ff). The command pdb2gmx works fine for the 5.1.2 version of gromacs but not for the 2016.3 version. The 2016.3 version is a local installation in my /home/user folder. The log shows the correct paths but does not consider my custom .rtp file. I would recommend to check whether the rtp file location and source where gmx you have installed match. Apart from that I do not think any error with version of Gromacs. Am i doing something wrong with the newer version? I added two simple files of my problem. Thanks in advance. Cheers Momin Ahmad Karlsruher Institut of Technology Germany -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Error in itp file
Hi Can you tell me, how have you used ACPYPE for itp. On Aug 2, 2017 9:36 AM, "Souvik Dey" wrote: > Hi, > > I just generated an itp file from ACPYPE. However, if I try to add ions it > shows the following error: > > Fatal error: > Syntax error - File FAD.itp, line 3 > Last line read: > '[ atomtypes ]' > Invalid order for directive atomtypes > > > Can somebody say how do I fix this? > > Regards, > Souvik Dey > > -- > Souvik Dey > Integrated Science Education & Research Centre > Visva Bharati University > Santiniketan-731235 > West Bengal > 8981736643 > -- > 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] Error in itp file
Hi, I just generated an itp file from ACPYPE. However, if I try to add ions it shows the following error: Fatal error: Syntax error - File FAD.itp, line 3 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes Can somebody say how do I fix this? Regards, Souvik Dey -- Souvik Dey Integrated Science Education & Research Centre Visva Bharati University Santiniketan-731235 West Bengal 8981736643 -- 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] Fwd: meaning of -sigfac option in gmx sigeps
Hi Everyone, Can anyone help me regarding the -sigfac option in gmx sigeps? What does this -sigfac imply? The LJ potential form is U(r) = (27/4)*epsilon [ (sigma/r)^9 - (sigma/r)^6 ] -- Tamisra Pal Post Doctoral Research Fellow Technische Universität Darmstadt Institut für Festkörperphysik Hochschulstraße 6 64289 Darmstadt , Germany -- 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] LINCS warning during energy minimization of nitrogen with virtual site
Dear all, Thank you for helping me. All I get from grompp is this -- gmx grompp -f grompp.mdp -c N2_box.gro -po mdout.mdp -p topol.top -o topol.tpr Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# NOTE 1 [file grompp.mdp]: The group cutoff scheme is deprecated since GROMACS 5.0 and will be removed in a future release when all interaction forms are supported for the verlet scheme. The verlet scheme already scales better, and it is compatible with GPUs and other accelerators. Setting the LD random seed to 1000542586 Generated 120 of the 120 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 120 of the 120 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'N_2' Cleaning up constraints and constant bonded interactions with virtual sites Analysing residue names: There are: 2493 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group System is 12462.00 NOTE 2 [file grompp.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. Largest charge group radii for Van der Waals: 0.056, 0.056 nm Largest charge group radii for Coulomb: 0.056, 0.056 nm This run will generate roughly 90 Mb of data There were 2 notes Back Off! I just backed up topol.tpr to ./#topol.tpr.1# gcq#454: "I never see what has been done; I only see what remains to be done." (Marie Curie) On Tue, Aug 1, 2017 at 5:08 PM, Justin Lemkul wrote: > > > On 8/1/17 6:07 PM, Ali Ahmed wrote: > >> Dear Dr. Dallas, >> Thank you for your reply. Actually, I'm new to GROMACS and >> I appreciate your support. >> >> >> -- >> Here is what I get before crashing. Too many warning then crush. >> >> > This is not diagnostic of anything useful. You've been asked several > times to provide the output of grompp, not mdrun. The grompp output can be > suggestive of issues you may not have considered. > > -Justin > > > Step 37, time 0.037 (ps) LINCS WARNING >> >> relative constraint deviation after LINCS: >> >> rms 0.002768, max 0.195102 (between atoms 34930 and 34931) >> >> bonds that rotated more than 30 degrees: >> >> atom 1 atom 2 angle previous, current, constraint length >> >> 193194 51.70.1100 0.1100 0.1100 >> >>54409 54410 32.30.1100 0.1100 0.1100 >> >> On Tue, Aug 1, 2017 at 4:49 PM, Dallas Warren >> wrote: >> >> Copy the output from both of those commands, most importantly (as Mark >>> has asked) that from the first one gmx grompp >>> >>> You need to show people exactly what you are seeing, not what you say >>> you are seeing. The latter you are filtering it, and most likely not >>> providing all the important information. The former allows those >>> trying to help to see all the information that they need to see. >>> Catch ya, >>> >>> Dr. Dallas Warren >>> Drug Delivery, Disposition and Dynamics >>> Monash Institute of Pharmaceutical Sciences, Monash University >>> 381 Royal Parade, Parkville VIC 3052 >>> dallas.war...@monash.edu >>> - >>> When the only tool you own is a hammer, every problem begins to resemble >>> a >>> nail. >>> >>> >>> On 2 August 2017 at 04:05, Ali Ahmed wrote: >>> Hi, Thank you for your help. well I used this command gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr gmx mdrun -v -deffnm em and I got all the warnings. Here is my em.mdp >>> - >>> integrator = steep emtol = 10.0 emstep = 0.001 nsteps = 5 energygrps = system ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 cutoff-scheme = group ns_type= grid coulombtype= PME rcoulomb = 1.0 rvdw= 1.0 pbc = xyz On Tue, Aug 1, 2017 at 11:07 AM, Mark Abraham >>> > wrote: Hi, > > No, only mdrun issues LINCS warnings. grompp issues different warnings, > and >>> I would like you to check whether you had any from grompp that you may > not >>> have considered. :-) > > Mark > > On Tue, Aug 1, 2017 at 5:04 PM Ali Ahmed wrote: > > Dear Mark >> Yes, all the warning
[gmx-users] Dynamics only for cavity in molecule.
Hello! I want to run dynamics only for a relatively small cavity of my molecule, with all other atoms frozen. For this reason, I also don't use solvent, because it won't move anyway. I run the simulation on GPU (gromacs 5.1.2), i.e. I use the Verlet scheme, pbc = xyz. However, when I start running simulations, I get violent behavior: the molecule immediately falls apart!! I am sure that I just made a silly thing in the parameters, but what is it? Here I attach my dynamics .mdp parameters: define = -DPOSRES integrator = md dt = 0.001 nsteps = 120 nstxout = 1000 nstvout = 1000 nstxtcout = 1000 nstlog = 100 nstenergy = 1000 continuation = no constraints= none tcoupl = V-rescale tc_grps = System tau_t = 0.1 ref_t = 0 cutoff-scheme = Verlet ns_type = grid nstlist = 10 rcoulomb = 0.9 rvdw = 0.9 coulombtype = PME pme_order = 4 fourierspacing = 0.16 pbc = xyz gen_vel = no DispCorr = EnerPres ; ; Freezing atoms # this is all the atoms except for the cavity inside ; freezegrps = GroupDyna freezedim = Y Y Y ; ; Heating ; annealing = single annealing_npoints = 2 annealing_time = 0 50 annealing_temp = 0 298 Thank you in advance, Dmitrii. -- 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] QM/MM in Gromacs-5.1.4?
Hello, I would like to use ORCA as a QM engine for Gromacs QM/MM simulation. I am just wondering shall we add additional options to cmake when we compile Gromacs? Thanks a lot Albert -- 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] GPU job failed
yes, the normal MD works fine. Even in a CPU based plumed also works. It seems that this function doesn't support PLumed GPU running? On 08/02/2017 01:02 PM, Mark Abraham wrote: Hi, My first guess is that the implementation of PLUMED doesn't support this. Does a normal non-PLUMED simulation run correctly when called in this manner? Mark -- 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] hole in the simulation box
thank you for your suggestion, I've tuned the gmx solvate -radius parameter until I achieved the stability of the box dimensions in the NPT ensemble, now it seem the everything is working... thanks again, regards, Emiliano On 2017-08-01 00:10, Dallas Warren wrote: There are insufficient waters in the box to fill it up completely. Two solutions that come to mind, add more water so it reaches the appropriate simulated density under those conditions, or run under NPT until reaches appropriate simulated density then swap back to NVT. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On 31 July 2017 at 18:14, edesantis wrote: Hi gromacs users, I am trying to simulate a crystal supershell (5x5x5 unit cells) with martini ff in gromacs 5. I build the system in aa representation, then I converted it in CG using the martinize.py script, following the tutorial, I've done a brief equilibration in water, the after the solvatation of the system with non-polarizable water, I've perform another energy minimization followed by the equilibration. then I've performed md simulation in the NVT ensemble. It happened that during the first steps of md, an empty (no protein no water) hole was created in my simulation box. during the md simulation the hole size became bigger (this hole doesn't appear if I do the simulation in NPT, but I'd prefer to avoid this ensemble since a dynamic volume of the box could alter the reticolar parameters of my crystal), I've tried to calculate forces using different algorithms but the hole is formed every time. the density of my system is 1.1 times the experimental one. Do you have an idea of the reason why I found this hole? do you have any suggestion to avoid its formation?? thank you in advance, regards Emiliano De Santis -- Emiliano De Santis -- 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. -- Emiliano De Santis -- 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] Error in the replica order in REMD (GMX v2016.1)
I solved it rather the brute force way: In the shell script which I
execute to run all my simulations I defined a variable for my Multidir
and filled it with all the directories (which were then in order).
somewhere in the shell script:
[...]
MULTIDIR=""
LAMBDALIST=(0 1 2 3 4 5)
$MDRUN=Your_Individua_MDrun_command
$FREE_ENERGY=YOUR_INDIVIDUAL_DIRECTORY
for i in ${LAMBDALIST[@]}; do
LAMBDA=$i
cd $FREE_ENERGY
mkdir Lambda_$LAMBDA
cd $FREE_ENERGY/Lambda_$LAMBDA
mkdir Production_MD
cd Production_MD
MULTIDIR="$MULTIDIR $FREE_ENERGY/Lambda_$LAMBDA/Production_MD"
done
$MDRUN -v -deffnm fec -multidir $MULTIDIR -replex 1000
You can adapt this for your needs.
On 02.08.2017 13:11, Mark Abraham wrote:
Hi,
The shell expansion is sorted alphabetically, rather than numerically, so
the order is md_0, md_1, md_10, md_11, etc. Either make your directories
like md_000, md_001, md_002, so the sortings are the same, or use a more
complex wildcard like -multidir md_[0-9] md_[1-9][0-9]
Mark
On Wed, Aug 2, 2017 at 1:06 PM ABEL Stephane wrote:
Hello again
Thanks to J. Hermann I can start my simulations, however few seconds
after the beginning of the run I have the following error
"Replicas with indices 2 < 12 have temperatures 271.9 > 254.27, please
order your replicas on increasing temperature"
I do not understand this error, since my replicas seem well ordered (i
think) : ref_t in replicas 2 is 254.27 K and ref_t in replicas 12 is
271.9) I check this with the ref_t in the mdp. For this calculation I used
the cpt file to generate the tpr.
Could you help me again ?
Stéphane
Stéphane Abel, Ph.D.
CEA Saclay DSV/ISVFJ/SB2SM
Institut de Biologie Intégrative de la Cellule (I2BC)
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60 <+33%206%2049%2037%2070%2060>
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__
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*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Boltzmannstr. 15
D-85748 Garching
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Fax: +49 8928915714
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Re: [gmx-users] Error in the replica order in REMD (GMX v2016.1)
Hi, The shell expansion is sorted alphabetically, rather than numerically, so the order is md_0, md_1, md_10, md_11, etc. Either make your directories like md_000, md_001, md_002, so the sortings are the same, or use a more complex wildcard like -multidir md_[0-9] md_[1-9][0-9] Mark On Wed, Aug 2, 2017 at 1:06 PM ABEL Stephane wrote: > Hello again > > Thanks to J. Hermann I can start my simulations, however few seconds > after the beginning of the run I have the following error > > "Replicas with indices 2 < 12 have temperatures 271.9 > 254.27, please > order your replicas on increasing temperature" > > I do not understand this error, since my replicas seem well ordered (i > think) : ref_t in replicas 2 is 254.27 K and ref_t in replicas 12 is > 271.9) I check this with the ref_t in the mdp. For this calculation I used > the cpt file to generate the tpr. > > Could you help me again ? > > Stéphane > > > > > Stéphane Abel, Ph.D. > > CEA Saclay DSV/ISVFJ/SB2SM > Institut de Biologie Intégrative de la Cellule (I2BC) > Bat 528, Office 138C > Gif-sur-Yvette, F-91191 FRANCE > Phone (portable) : +33 6 49 37 70 60 <+33%206%2049%2037%2070%2060> > -- > 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] Error in the replica order in REMD (GMX v2016.1)
Hello again Thanks to J. Hermann I can start my simulations, however few seconds after the beginning of the run I have the following error "Replicas with indices 2 < 12 have temperatures 271.9 > 254.27, please order your replicas on increasing temperature" I do not understand this error, since my replicas seem well ordered (i think) : ref_t in replicas 2 is 254.27 K and ref_t in replicas 12 is 271.9) I check this with the ref_t in the mdp. For this calculation I used the cpt file to generate the tpr. Could you help me again ? Stéphane Stéphane Abel, Ph.D. CEA Saclay DSV/ISVFJ/SB2SM Institut de Biologie Intégrative de la Cellule (I2BC) Bat 528, Office 138C Gif-sur-Yvette, F-91191 FRANCE Phone (portable) : +33 6 49 37 70 60 -- 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] GPU job failed
Hi, My first guess is that the implementation of PLUMED doesn't support this. Does a normal non-PLUMED simulation run correctly when called in this manner? Mark On Wed, Aug 2, 2017 at 9:55 AM Albert wrote: > Hello, > > I am trying to run Gromacs with the following command line: > > > mpirun -np 4 gmx_mpi mdrun -v -g 7.log -s 7.tpr -x 7.xtc -c 7.gro -e > 7.edr -plumed plumed.dat -ntomp 2 -gpu_id 0123 > > but it always failed with the following messages: > > Running on 1 node with total 24 cores, 48 logical cores, 4 compatible GPUs > Hardware detected on host cudaC.europe.actelion.com (the node of MPI > rank 0): >CPU info: > Vendor: GenuineIntel > Brand: Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz > SIMD instructions most likely to fit this hardware: AVX2_256 > SIMD instructions selected at GROMACS compile time: AVX2_256 >GPU info: > Number of GPUs detected: 4 > #0: NVIDIA GeForce GTX TITAN X, compute cap.: 5.2, ECC: no, stat: > compatible > #1: NVIDIA GeForce GTX TITAN X, compute cap.: 5.2, ECC: no, stat: > compatible > #2: NVIDIA GeForce GTX TITAN X, compute cap.: 5.2, ECC: no, stat: > compatible > #3: NVIDIA GeForce GTX TITAN X, compute cap.: 5.2, ECC: no, stat: > compatible > > Reading file 7.tpr, VERSION 5.1.3 (single precision) > Changing nstlist from 20 to 40, rlist from 1.02 to 1.08 > > Using 4 MPI processes > Using 2 OpenMP threads per MPI process > > On host cudaC.europe.actelion.com 4 compatible GPUs are present, with > IDs 0,1,2,3 > On host cudaC.europe.actelion.com 4 GPUs auto-selected for this run. > Mapping of GPU IDs to the 4 PP ranks in this node: 0,1,2,3 > > > --- > Program gmx mdrun, VERSION 5.1.3 > Source code file: > /home/albert/Downloads/gromacs/gromacs-5.1.3/src/gromacs/mdlib/nbnxn_cuda/ > nbnxn_cuda_data_mgmt.cu, > line: 403 > > Fatal error: > cudaCreateTextureObject on nbfp_texobj failed: invalid argument > > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > --- > > Does anybody have any idea what's happening? > > THX a lot. > > -- > 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] -multidir option in REMD (GROMACS v2016.1)
Hi,
On Wed, Aug 2, 2017 at 11:22 AM ABEL Stephane wrote:
> Dear all,
>
> I would like to do a REMD of a system with 75 replicas (with 75
> directories named md_0,..., md_75) and I have two questions.
>
> 1) To launch the md calculation we should use the followng command :
>
> mpirun -np 4 mdrun_mpi -v -multidir sim[0123] -replex XXX
>
> My question is since I have 75 replicas (directories). How I should set
> the argument of -multidir ? Like this : -multidir md_[01234...75] or only
> "md_".
>
The -multidir option needs a list of all your directories. The best way to
do that is with shell (e.g. wildcard) expansion. Just using "md_" doesn't
get expanded by anything. I recently observed someone suggest that
"md_{0..75}" might do what you want, but I've never tried it. Anyway, md_*
will expand them all, and IIRC mdrun will sort out the ordering from the
values of the REMD control parameter.
> I have used the following command : mdrun_mpi -v -multidir
> ./"$Stage1_FileName"/md_ -replex 500, but the program stops with the
> following error : Need at least two replicas for replica exchange (option
> -multi)
>
Since there's only one directory named, because the shell couldn't expand
anything for you, mdrun doesn't know how to proceed. Pro tip - get it
working for a small number of replicas (e.g. 2) before worrying about using
all 75.
> 2) Second question It is not clear to me how I should set the number of
> step in the mdp file of each replica use in the production runs. For
> instance I want to do a simulation of 50 ns, should I set nsteps =
> 500/75
>
Each simulation is independent and every e.g. mdp parameter is particular
to it. So choose your number of steps in each mdp file to be the length of
a single replica. Obviously nsteps * dt = time in the usual way, but since
we don't know dt, you'll have to compute your nsteps ;-)
Mark
Could you help me ?
>
> Thanks for your help
>
> Stéphane
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Re: [gmx-users] -multidir option in REMD (GROMACS v2016.1)
Hi, On 02.08.2017 11:21, ABEL Stephane wrote: Dear all, I would like to do a REMD of a system with 75 replicas (with 75 directories named md_0,..., md_75) and I have two questions. 1) To launch the md calculation we should use the followng command : mpirun -np 4 mdrun_mpi -v -multidir sim[0123] -replex XXX My question is since I have 75 replicas (directories). How I should set the argument of -multidir ? Like this : -multidir md_[01234...75] or only "md_". the .tpr file should be called same, e.g. md.tpr, then try: -dffnm md - multidir YOURPATHBEFORE/md_* The "*" fills all the available lambdas I have used the following command : mdrun_mpi -v -multidir ./"$Stage1_FileName"/md_ -replex 500, but the program stops with the following error : Need at least two replicas for replica exchange (option -multi) 2) Second question It is not clear to me how I should set the number of step in the mdp file of each replica use in the production runs. For instance I want to do a simulation of 50 ns, should I set nsteps = 500/75 You set the steps for each replica in the mdp file. E.g. nsteps = 500 Will simulate each replica for 50ns Could you help me ? Thanks for your help Stéphane All the best Johannes -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] -multidir option in REMD (GROMACS v2016.1)
Dear all, I would like to do a REMD of a system with 75 replicas (with 75 directories named md_0,..., md_75) and I have two questions. 1) To launch the md calculation we should use the followng command : mpirun -np 4 mdrun_mpi -v -multidir sim[0123] -replex XXX My question is since I have 75 replicas (directories). How I should set the argument of -multidir ? Like this : -multidir md_[01234...75] or only "md_". I have used the following command : mdrun_mpi -v -multidir ./"$Stage1_FileName"/md_ -replex 500, but the program stops with the following error : Need at least two replicas for replica exchange (option -multi) 2) Second question It is not clear to me how I should set the number of step in the mdp file of each replica use in the production runs. For instance I want to do a simulation of 50 ns, should I set nsteps = 500/75 Could you help me ? Thanks for your help Stéphane -- 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] Clayff forcefield
I try to implement CLYFF in gromacs. I created ffbonded.itp, ffnonbonded.itp, atomtype.atp, forcefield.doc, forcefield.itp and molecule.rtp. I want to simulate Kaolinite, and I try to use pdb2gmx to create a topology. My first question is that should I create any other files? second, In molecule.rtp, I just write the atom type, atom name and charges. should I add bonds for each atom? Also, in rtp file, I don't know what should I write as a residue? Thank you in advance, Golnaz -- 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] Creating Custom .rtp files
I think the reason for the weird log is the "|&tee" command that lets you write the output of another command into a file. In the case of the error i could choose the forcefield before the error occurred. The methane was called "CH4" before, i just changed the names for troubleshooting. This time i did copy&paste manually. Files are attached. There are two comments that show the differences in the versions. Again: the two .rtp files for both versions are identical and the same .pdb file is used. Am 01.08.2017 um 20:42 schrieb Justin Lemkul: On 8/1/17 10:32 AM, Momin Ahmad wrote: please finde the files attached to this email: log-files for the 5.1.2 version and the 2016.3 version, also again the .rtp file and the .pdb file The screen output seems garbled to me, with the fatal error coming before the force field selection, and multiple locations being used. I can't figure out what's going on. Your .rtp needs to be in the force field directory that you choose, either locally (within the working directory) or system-wide (wherever that is installed). Note also that "CH4" and "CH41" are different, because one error indicates that pdb2gmx finds CH4 when your .rtp is clearly CH41. -Justin Am 01.08.2017 um 00:48 schrieb Justin Lemkul: On 7/31/17 7:47 AM, Momin Ahmad wrote: Hello, the .rtp file is located in the same directory as the force-field. When i type gmx gmx2pdb . then the log shows that the right path is considered and loads the needed .rtp fiels that already exist in the forc-field file. But my custom one is ignored. Please post the full screen output of pdb2gmx, including the force field selection. If your .rtp file is not being read, it is likely misformatted, in which case you should either write your new residue entries in an existing file or upload it to a file-sharing service so we can provide feedback. -Justin Greets Momin Ahmad Am 25.07.2017 um 16:34 schrieb RAHUL SURESH: On Tue, 25 Jul 2017 at 5:58 PM, Momin Ahmad wrote: Hi, I created a custom .pdb file and the associated .rtp file for the force-field (amber99sb-ildn.ff). The command pdb2gmx works fine for the 5.1.2 version of gromacs but not for the 2016.3 version. The 2016.3 version is a local installation in my /home/user folder. The log shows the correct paths but does not consider my custom .rtp file. I would recommend to check whether the rtp file location and source where gmx you have installed match. Apart from that I do not think any error with version of Gromacs. Am i doing something wrong with the newer version? I added two simple files of my problem. Thanks in advance. Cheers Momin Ahmad Karlsruher Institut of Technology Germany -- 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. -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu :-) GROMACS - gmx pdb2gmx, VERSION 5.1.2 (-: GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. BerendsenPar Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch Gerrit Groenhof Christoph Junghans Anca HamuraruVincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter TielemanTeemu Virolainen Christian WennbergMaarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2015, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx pdb2gmx, VERSION 5.1.2 Executable: /usr/bin/gmx Data prefix: /usr Command line: gmx pdb2gmx -f methane.pdb Select the Force Field: From '/usr/share/gromacs/top': 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 2: AMBER94 force field (Cornell et al., JACS 117
[gmx-users] membrane-protein simulation
Hello gmx-user I want to simulate a membrane protein with more than one chains like A, B, C etc. I generated the strong_posre.itp file as Justing has kindly explained in his tutorial, and updated the topol.top file by inserting the same lines. I also updated the minim.mdp file by inserting STRONG_POSRES. Once I tried the minimization of the system before the shrinking step, I got the error as below: Fatal error: [ file strong_posre.itp, line 548 ]: Atom index (544) in position_restraints out of bounds (1-543). This probably means that you have inserted topology section "position_restraints" in a part belonging to a different molecule than you intended to. In that case move the "position_restraints" section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I tried so many options but could not fix the issue. Please keep in view that the same procedure is working well with a single chain of the protein. Kindly help me how to fix this issue? Thanks in advance -- 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] GPU job failed
Hello, I am trying to run Gromacs with the following command line: mpirun -np 4 gmx_mpi mdrun -v -g 7.log -s 7.tpr -x 7.xtc -c 7.gro -e 7.edr -plumed plumed.dat -ntomp 2 -gpu_id 0123 but it always failed with the following messages: Running on 1 node with total 24 cores, 48 logical cores, 4 compatible GPUs Hardware detected on host cudaC.europe.actelion.com (the node of MPI rank 0): CPU info: Vendor: GenuineIntel Brand: Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz SIMD instructions most likely to fit this hardware: AVX2_256 SIMD instructions selected at GROMACS compile time: AVX2_256 GPU info: Number of GPUs detected: 4 #0: NVIDIA GeForce GTX TITAN X, compute cap.: 5.2, ECC: no, stat: compatible #1: NVIDIA GeForce GTX TITAN X, compute cap.: 5.2, ECC: no, stat: compatible #2: NVIDIA GeForce GTX TITAN X, compute cap.: 5.2, ECC: no, stat: compatible #3: NVIDIA GeForce GTX TITAN X, compute cap.: 5.2, ECC: no, stat: compatible Reading file 7.tpr, VERSION 5.1.3 (single precision) Changing nstlist from 20 to 40, rlist from 1.02 to 1.08 Using 4 MPI processes Using 2 OpenMP threads per MPI process On host cudaC.europe.actelion.com 4 compatible GPUs are present, with IDs 0,1,2,3 On host cudaC.europe.actelion.com 4 GPUs auto-selected for this run. Mapping of GPU IDs to the 4 PP ranks in this node: 0,1,2,3 --- Program gmx mdrun, VERSION 5.1.3 Source code file: /home/albert/Downloads/gromacs/gromacs-5.1.3/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.cu, line: 403 Fatal error: cudaCreateTextureObject on nbfp_texobj failed: invalid argument For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Does anybody have any idea what's happening? THX a lot. -- 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.
