[gmx-users] Topology for covalent bonds across periodic boundaries
Dear Gromacs users, I am trying to simulate an "infinite" protein chain by covalently bonding the last residue of my structure to the first residue across the periodic boundary. I have modified the topology file to include these bonded interactions and have specified "periodic-molecules=yes" in my mdp file. However, when attempting to use grompp, I get many errors of the type "No default Bond types" "No default U-B types" etc. Below is a snippet of the first residue of my structure: 0ALA N1 -2.130 11.857 5.885 0ALA HN2 -2.194 11.930 5.907 0ALA CA3 -2.193 11.725 5.916 And a snippet of the last residue: 179THR HG23 2660 3.379 11.851 6.387 179THR C 2661 3.583 11.711 6.162 179THR O 2662 3.514 11.783 6.087 I have identified and added ~30 bonded interactions to my topology file. For example, the carbon in THR should be bonded to the nitrogen in ALA, so I have added the following line (line #5541 in my .top file): [ bonds ] ; aiaj functc0c1c2c3 2661 1 1 However, grompp returns the following error: ERROR 1 [file monomer_3.top, line 5541]: No default Bond types Similar errors are produced for most (but not all) of the added interactions. All of the "pairs" and four of the "dihedrals" were processed without errors. I cannot find a pattern in the dysfunctional vs functional lines. For example, the following dihedral did not return an error: (179THR N 2649 )-(179THR CA 2651 )-(179THR C 2661 )-(0ALA N1 ) However, this dihedral did: (179THR CA 2651 )-(179THR C 2661 )-(0ALA N1 )-(0ALA HN2 ) Any help in debugging this would be much appreciated! Thanks in advance, Rachel Baarda -- 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] 2019.2 build warnings
Okay, more interesting things are happening. At the end of 'make' I get a bunch of things like .. nbnxn_cuda.cu(373): warning: variable "dim_grid" was declared but never referenced -bash: syntax error near unexpected token `373' More errors during 'make check' right after " Building NVCC (Device) object src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o" then continues as if nothing happened. Finally, fails test #42 with what appears to be sarcasm: "... Thanx for Using GROMACS - Have a Nice Day Mdrun cannot use the requested (or automatic) number of ranks, retrying with 8. Abnormal return value for ' gmx mdrun-nb cpu -notunepme >mdrun.out 2>&1' was 1 Retrying mdrun with better settings... Abnormal return value for ' gmx mdrun -ntmpi 1 -notunepme >mdrun.out 2>&1' was -1 FAILED. Check mdrun.out, md.log file(s) in distance_restraints for distance_restraints Abnormal return value for ' gmx mdrun -ntmpi 6 -notunepme >mdrun.out 2>&1' was 1 Retrying mdrun with better settings... Abnormal return value for ' gmx mdrun -notunepme >mdrun.out 2>&1' was -1 FAILED. Check mdrun.out, md.log file(s) in octahedron for octahedron Re-running orientation-restraints using CPU-based PME Abnormal return value for ' gmx mdrun -ntmpi 1 -pme cpu-notunepme >mdrun.out 2>&1' was -1 FAILED. Check mdrun.out, md.log file(s) in orientation-restraints/pme-cpu for orientation-restraints-pme-cpu Re-running pull_geometry_angle using CPU-based PME Re-running pull_geometry_angle-axis using CPU-based PME Re-running pull_geometry_dihedral using CPU-based PME 3 out of 55 complex tests FAILED" Then finally quits for good. Your suggestions will be highly appreciated. 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.
[gmx-users] 2019.2 build warnings
Hi all, I am building the 2019.2 version, latest CUDA libs (older 2018 version works fine). While building, I am getting a ton of warnings as shown below, while the build does not terminate. Is this okay, or do we need to do anything at this point? Thanks, Alex localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning: variable "dim_grid" was declared but never referenced localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning: variable "dim_block" was declared but never referenced localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning: variable "dim_grid" was declared but never referenced localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning: variable "dim_block" was declared but never referenced localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning: variable "dim_grid" was declared but never referenced localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning: variable "dim_block" was declared but never referenced localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning: variable "dim_grid" was declared but never referenced localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning: variable "dim_block" was declared but never referenced localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning: variable "dim_grid" was declared but never referenced localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning: variable "dim_block" was declared but never referenced localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning: variable "dim_grid" was declared but never referenced localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning: variable "dim_block" was declared but never referenced localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning: variable "dim_grid" was declared but never referenced localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning: variable "dim_block" was declared but never referenced localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning: variable "dim_grid" was declared but never referenced localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning: variable "dim_block" was declared but never referenced localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning: variable "dim_grid" was declared but never referenced -- 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] Nonzero phase angles
Dear all How can I translate the OPLS parameters to Ryckaert-Bellemans parameters (C0,C1,C2,C3,...) when the phase angles (f1,f2,f3,f4) are not zero. V=V0/2+V1/2(1-cos(Q-f1))+V2/2(1-cos(Q-f2))+V3/2(1-cos(Q-f3))+V4/2(1-cos(Q-f4)) Many thanks -- This email was Anti Virus checked by Security Gateway. -- 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] Generalized Energy Groups
Hi all, I'm currently trying to analyze the energy balance of a trajectory where I see various kinds of spatial partitioning of my molecules. I'd like to be able see a breakdown based on spatial group and atom type. However, I only know which molecules end up in which spatial region after the trajectory is complete (so I can't just declare the groups beforehand in my mdp file). Likewise, I want some sort of intersection of atom type and spatial group for my analysis, but it seems that this sort of selection is more general than what I could do with the energy groups in an mdp file, and I can't use a more general index file with the gmx energy command post-simulation. Is there any way to do something like mdrun -rerun with more general groups of atom indices to get a customized breakdown of energetic interactions from a trajectory, or is this type of thing just not supported? Thanks, Tom Allen -- 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] Nonzero phase angles
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Re: [gmx-users] -ignh command removes protonation site of interest
On 4/16/19 3:21 PM, Neena Susan Eappen wrote: I am using OPLS-AA force field and there are no parameters for protonated carbonyl for alanine residue. How do I go about this? What exactly are you trying to protonate? The oxygen in a peptide bond is not protonated. The C-terminus can be neutralized by selecting the "COOH" terminus type interactively using -ter. -Justin Thank you, Neena From: Neena Susan Eappen Sent: Monday, April 15, 2019 10:30 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] -ignh command removes protonation site of interest Hello gromacs users, I started with a peptide where protonation site was on a carbonyl oxygen. However, using -ignh command in pdb2gmx, I lose that proton from there. Any insights on how to move forward? Many thanks, Neena -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] -ignh command removes protonation site of interest
I am using OPLS-AA force field and there are no parameters for protonated carbonyl for alanine residue. How do I go about this? Thank you, Neena From: Neena Susan Eappen Sent: Monday, April 15, 2019 10:30 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] -ignh command removes protonation site of interest Hello gromacs users, I started with a peptide where protonation site was on a carbonyl oxygen. However, using -ignh command in pdb2gmx, I lose that proton from there. Any insights on how to move forward? Many thanks, Neena -- 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
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 -- 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
Hi Emilio, > Is there a way of doing it using gromacs tools? Perhaps you can use gmx genconf? http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-genconf.html Have a look and see if it would work for you. I'm sure there are other ways that may be better, but this is the first that comes to mind. -John -- 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] increase membrane dimensions
Dear Gromacs users, I want to simulate a protein embedded in a membrane made of POPC phospholipid. I have some experience with MD, but it is the first time that I am simulating a membrane protein. I am following the tutorial of KALP15 in DPPC membrane (http://www.mdtutorials.com/gmx/membrane_protein/02_topology.html). my problem is that I want to simulate a bigger protein respect to the one in the tutorial and in order to avoid to have interactions among the replicas, I need to have also a bigger membrane (more than 128 lipids, that are in the equilibrated gro file) how can I increase the dimensions of the membrane? I could add (and subtract and the various combinations) to all the phospholipid coordinates the sides of my simulation box, but my fear is that in this way I would have collisions on the atoms at the box edges, Is there a way of doing it using gromacs tools? thank you in advance, best Emiliano -- 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.
Re: [gmx-users] Protein-Ligand interactions
Hi Use higher force constant and see what is happening On Tue 16 Apr, 2019, 6:14 PM RAHUL SURESH On Tue, Apr 16, 2019 at 1:57 PM Bratin Kumar Das < > 177cy500.bra...@nitk.edu.in> wrote: > > > Hi, > > The force you assigned for position restrain may not be enough to > hold > > the ligand in the proper position. If u follow the gromacs tutorial > ...the > > simulation method is not wrong. > > > > Thank you. I am sure, I haven't changed any step from the tutorial. Is > there any better option to hold the ligand and protein together? > > Thank you Mr. Das > > > > > On Tue 16 Apr, 2019, 11:22 AM RAHUL SURESH wrote: > > > > > Hi Users. > > > > > > A basic clarification on protein and small molecule interaction. > > > > > > I have a docked complex of a protein-ligand (to accept, the docking > score > > > is too low). On simulation, even after applying position restraint, I > > find > > > the ligand moving around the protein. Is this because there is any > error > > in > > > the simulation method or it might be due to low interaction between the > > > ligand and protien? any suggestions to understand this problem? > > > > > > Thank you > > > > > > -- > > > *Regards,* > > > *Rahul * > > > -- > > > 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. > > > > > -- > *Regards,* > *Rahul * > -- > 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] Make check error
Hi, I met some errors when running make check after compiling the Gromacs 2019. Really appreciate it if anyone could help me. The Cmake info is listed as below: cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_SIMD=AVX2_256 -DCMAKE_INSTALL_PREFIX=/home/sly1993/sly1993/software/gromacs_run -DGMX_MPI=on -DMPIEXEC=srun And I used intel/2018 and openmpi/3.0.0 to compile it. The compiling is success and I can install it to my home path. Because the HPC uses SLURM system so I need to run the gromacs by the following command: srun --mpi=pmix_v1 gmx_mpi It works and output lots of normal information. However, I met lots of errors when I run “make check” command because I want to check if the software works properly. The errors are listed as below: Test project /home/sly1993/sly1993/software/gromacs/gromacs-2019.1/build Start 1: TestUtilsUnitTests 1/46 Test #1: TestUtilsUnitTests ..***Failed0.15 sec -- The application appears to have been direct launched using "srun", but OMPI was not built with SLURM's PMI support and therefore cannot execute. There are several options for building PMI support under SLURM, depending upon the SLURM version you are using: version 16.05 or later: you can use SLURM's PMIx support. This requires that you configure and build SLURM --with-pmix. Versions earlier than 16.05: you must use either SLURM's PMI-1 or PMI-2 support. SLURM builds PMI-1 by default, or you can manually install PMI-2. You must then build Open MPI using --with-pmi pointing to the SLURM PMI library location. Please configure as appropriate and try again. -- *** An error occurred in MPI_Init_thread *** on a NULL communicator *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, ***and potentially your MPI job) [i21a-s1.ufhpc:15257] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed! Start 2: TestUtilsMpiUnitTests 2/46 Test #2: TestUtilsMpiUnitTests ...***Failed2.01 sec srun: error: Unable to create step for job 34989369: More processors requested than permitted Start 3: MdlibUnitTest 3/46 Test #3: MdlibUnitTest ...***Failed0.03 sec Abnormal return value for 'gmx_mpi grompp -f ./grompp.mdp -c ./conf -r ./conf -p ./topol -maxwarn 10 >grompp.out 2>grompp.err' was 1 No topol.tpr file in rb125. grompp failed FAILED. Check grompp.err, grompp.out file(s) in rb125 for rb125 16 out of 16 simple tests FAILED Start 42: regressiontests/complex ^Cmake[3]: *** [CMakeFiles/run-ctest-nophys] Interrupt make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Interrupt make[1]: *** [CMakeFiles/check.dir/rule] Interrupt make: *** [check] Interrupt I guess because the SLURM system adds the preflag “―mpi=pmix_v1” in the run so I may need to adjust the CMAKE command. Anyone can tell me how to adjust the Cmake command? Thank you very much in advance. Regards, Linyuan -- Linyuan Shi Ph.D. Candidate Materials Science Engineering Department University of Florida Cell: 352-283-9950 -- 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] Protein-Ligand interactions
On Tue, Apr 16, 2019 at 1:57 PM Bratin Kumar Das < 177cy500.bra...@nitk.edu.in> wrote: > Hi, > The force you assigned for position restrain may not be enough to hold > the ligand in the proper position. If u follow the gromacs tutorial ...the > simulation method is not wrong. > Thank you. I am sure, I haven't changed any step from the tutorial. Is there any better option to hold the ligand and protein together? Thank you Mr. Das > > On Tue 16 Apr, 2019, 11:22 AM RAHUL SURESH > > Hi Users. > > > > A basic clarification on protein and small molecule interaction. > > > > I have a docked complex of a protein-ligand (to accept, the docking score > > is too low). On simulation, even after applying position restraint, I > find > > the ligand moving around the protein. Is this because there is any error > in > > the simulation method or it might be due to low interaction between the > > ligand and protien? any suggestions to understand this problem? > > > > Thank you > > > > -- > > *Regards,* > > *Rahul * > > -- > > 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. > -- *Regards,* *Rahul * -- 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] GROMACS 2019.2 patch release available
Hello again, apologies for messing up the subject line, this is of course for the 2019.2 point release! Cheers Paul On 16/04/2019 13:41, Paul bauer wrote: Hi GROMACS users, The official release of GROMACS 2019.2 is available! This second patch release fixes several issues found since the last patch release of GROMACS 2019. We encourage all users of the 2019 series to update to 2019.2. Please see the link to the release notes below for more details. You can find the code, documentation, release notes, and test suite at the links below. Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2019.2.tar.gz Documentation: http://manual.gromacs.org/2019.2/index.html (including release notes, install guide, user guide, reference manual) Test Suite: http://gerrit.gromacs.org/download/regressiontests-2019.2.tar.gz Happy simulating! Paul -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737308594 -- 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] GROMACS 2019.1 patch release available
Hi GROMACS users, The official release of GROMACS 2019.2 is available! This second patch release fixes several issues found since the last patch release of GROMACS 2019. We encourage all users of the 2019 series to update to 2019.2. Please see the link to the release notes below for more details. You can find the code, documentation, release notes, and test suite at the links below. Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2019.2.tar.gz Documentation: http://manual.gromacs.org/2019.2/index.html (including release notes, install guide, user guide, reference manual) Test Suite: http://gerrit.gromacs.org/download/regressiontests-2019.2.tar.gz Happy simulating! Paul -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737308594 -- 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] calculation of pair wise interaction energy of residues
thank so much for your reply. Is there any loop which i can use to calculate all the residue pair wise interaction energy. So all the data can be handled. On Tue, Apr 16, 2019 at 2:29 PM Mark Abraham wrote: > Hi, > > You have to compute all the pairwise interactions if you want to compare > all the pairwise interactions. > > But I'm deeply skeptical that you can learn anything from this anyway. The > potential energy of typical force fields is not constructed to be > decomposable, and such an analysis neglects the entropic component of the > free energy anyway. > > Mark > > On Tue, 16 Apr 2019 at 07:52, SHAHEE ISLAM wrote: > > > hi, > > Is it possible to calculate pair wise interaction energy of each residue. > > My protein consist of 129 residue. Because if i mention each residue as a > > group in mdp file then i will get a huge number of data. Which is very > > difficult to handle. > > Can anyone please suggest me how i can do this. > > Thanking you > > Shahee > > -- > > 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.
[gmx-users] PCA with Gromacs
Dear Gmx users, I've been using Gromacs to perform Principal Component Analysis on my trajectories. 1- With gmx anaeig, we can plot a 2d projection of a trajectory on eigenvectors 1 and 2 (for example). I would like to know if there is a way to obtain the same plot but where the points are color-coded according to MD time? 2-I also would like to know how the diagonalization of the covariance-matrix with gmx covar is done: Is it by Eigenvalue decomposition (EVD) or Singular value decomposition (SVD)? I couldn't find the information on the manual... Thank you in advance for your help. Zeineb -- 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] -ignh command removes protonation site of interest
Or another way to keep the protonated state of residue is using -asp, -glu, -his ... and then you can manually assign the protonation state On Tue, Apr 16, 2019 at 1:06 AM Justin Lemkul wrote: > > > On 4/15/19 6:30 PM, Neena Susan Eappen wrote: > > Hello gromacs users, > > > > I started with a peptide where protonation site was on a carbonyl > oxygen. However, using -ignh command in pdb2gmx, I lose that proton from > there. Any insights on how to move forward? > > If you want another protonation state, then you need to make sure the > residue is named as expected by the force field (e.g. ASPP for > protonated aspartate, not ASP, etc). > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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] standard error
Hi, I don't recall gmx analyze computing standard errors. But gmx analyze -h will report on what it does do :-) Does that help? Mark On Tue, 16 Apr 2019 at 08:58, Raag Saluja wrote: > Hi! > > What percent error is calculated as standard error by gmx analyze? 5%? > > Thank you in advance and regards, > Raag > -- > 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] calculation of pair wise interaction energy of residues
Hi, You have to compute all the pairwise interactions if you want to compare all the pairwise interactions. But I'm deeply skeptical that you can learn anything from this anyway. The potential energy of typical force fields is not constructed to be decomposable, and such an analysis neglects the entropic component of the free energy anyway. Mark On Tue, 16 Apr 2019 at 07:52, SHAHEE ISLAM wrote: > hi, > Is it possible to calculate pair wise interaction energy of each residue. > My protein consist of 129 residue. Because if i mention each residue as a > group in mdp file then i will get a huge number of data. Which is very > difficult to handle. > Can anyone please suggest me how i can do this. > Thanking you > Shahee > -- > 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] Protein-Ligand interactions
Hi, The force you assigned for position restrain may not be enough to hold the ligand in the proper position. If u follow the gromacs tutorial ...the simulation method is not wrong. On Tue 16 Apr, 2019, 11:22 AM RAHUL SURESH Hi Users. > > A basic clarification on protein and small molecule interaction. > > I have a docked complex of a protein-ligand (to accept, the docking score > is too low). On simulation, even after applying position restraint, I find > the ligand moving around the protein. Is this because there is any error in > the simulation method or it might be due to low interaction between the > ligand and protien? any suggestions to understand this problem? > > Thank you > > -- > *Regards,* > *Rahul * > -- > 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] standard error
Hi! What percent error is calculated as standard error by gmx analyze? 5%? Thank you in advance and regards, Raag -- 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.
