Re: [gmx-users] The maxwarn fatal errors
On 1/6/20 9:40 PM, 변진영 wrote: Dear everyone, Happy New year! I have gone through the Justin Lemku tutorial for Umbrella Sampling. During tutorial, When I treid to input the command line: gmx grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -r npt0.gro -n index.ndx -o umbrella0.tpr I have met two warnings and they occured fatal error.: Fatal error: Too many warnings (2). If you are sure all warnings are harmless, use the -maxwarn option. And the waring is: WARNING 1 [file topol.top, line 56]: The GROMOS force fields have been parametrized with a physically incorrect multiple-time-stepping scheme for a twin-range cut-off. When used with a single-range cut-off (or a correct Trotter multiple-time-stepping scheme), physical properties, such as the density, might differ from the intended values. Since there are researchers actively working on validating GROMOS with modern integrators we have not yet removed the GROMOS force fields, but you should be aware of these issues and check if molecules in your system are affected before proceeding. Further information is available at https://redmine.gromacs.org/issues/2884 , and a longer explanation of our decision to remove physically incorrect algorithms can be found at https://doi.org/10.26434/chemrxiv.11474583.v1 . WARNING 2 [file md_umbrella.mdp]: With Nose-Hoover T-coupling and Parrinello-Rahman p-coupling, tau-p (1) should be at least twice as large as tau-t (1) to avoid resonances I solved this problem with using -maxwarn option but I am wondering whether thses warning is passed over. What do you think what I happend? dears. Any idea on what caused this problem? The first warning is very verbose and provides you with substantial justification and background reading. As for the second, change tau-p to 2 as suggested. Note that I have not made any attempt to update the tutorials for the 2020 version, and they are only guaranteed to be compatible with GROMACS 2018.x versions. -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.
[gmx-users] The maxwarn fatal errors
Dear everyone, Happy New year! I have gone through the Justin Lemku tutorial for Umbrella Sampling. During tutorial, When I treid to input the command line: gmx grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -r npt0.gro -n index.ndx -o umbrella0.tpr I have met two warnings and they occured fatal error.: Fatal error: Too many warnings (2). If you are sure all warnings are harmless, use the -maxwarn option. And the waring is: WARNING 1 [file topol.top, line 56]: The GROMOS force fields have been parametrized with a physically incorrect multiple-time-stepping scheme for a twin-range cut-off. When used with a single-range cut-off (or a correct Trotter multiple-time-stepping scheme), physical properties, such as the density, might differ from the intended values. Since there are researchers actively working on validating GROMOS with modern integrators we have not yet removed the GROMOS force fields, but you should be aware of these issues and check if molecules in your system are affected before proceeding. Further information is available at https://redmine.gromacs.org/issues/2884 , and a longer explanation of our decision to remove physically incorrect algorithms can be found at https://doi.org/10.26434/chemrxiv.11474583.v1 . WARNING 2 [file md_umbrella.mdp]: With Nose-Hoover T-coupling and Parrinello-Rahman p-coupling, tau-p (1) should be at least twice as large as tau-t (1) to avoid resonances I solved this problem with using -maxwarn option but I am wondering whether thses warning is passed over. What do you think what I happend? dears. Any idea on what caused this problem? -- 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] CMAP format on GROMCACS
On 1/6/20 4:46 PM, Marcelo Depólo wrote: Hi everybody! Happy new year! =) I would like to understand a little bit better the CMAP format of charmm27.ff within GROMACS. I've looked up in the manual but found little information. I understand that it is defined by 5 atoms (1-4 phi and 2-5 psi), a arbitrary identification number (e.g. 1) and the grid size (e.g. 24x24). But the following grid values are lines with just 10 values each, ended with a "\", instead of a 24 columns- 24 lines matrix. How are those values of CMAP formatted in GMX? Does GMX automatically transform those values in a matrix and, if so, can I consider that its "y-axis" would be PSI and "x-axis" would be PHI? The \ are line continuation characters, so GROMACS is reading a 24x24 matrix in a single array of values. The values are written for all values of phi at a given value of psi, i.e. writing each row of the matrix, starting from phi = -180, psi = -180 until phi = 180, psi = 180. -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.
Re: [gmx-users] atom moved too far
On 1/6/20 2:59 PM, Christos Deligkaris wrote:
Justin, thank you.
I have implemented the pull code but that also exhibits the same error when
I use 12 cores (failed at about 2ns) and the simulation goes on fine when I
use 6 cores (now at about 32 ns).
I tried using the v-rescale thermostat (instead of Nose-Hoover) and
Parinello-Rahman barostat, which failed. I also tried the v-rescale
thermostat and the Berendsen barostat but that also failed. It seems to me
that this is not an equilibration issue.
So, to summarize, only if I decrease the time step to 0.001 ps or decrease
the number of cores seem to allow the calculation to proceed.
In this email list, I read that someone else was trying to use different
arguments supplied to mdrun (-nt, -ntomp etc) to solve the same problem. Is
it possible that the problem arises due to my running gmx_mpi on a single
node? This is the command I use in my submission script:
mpirun --mca btl tcp,sm,self /opt/gromacs-2018.1/bin/gmx_mpi mdrun -ntomp
\$ntomp -v -deffnm "${inputfile%.tpr}"
If you think that this is not due to a physics issue I can continue doing
calculations with 6 cores and try to install gromacs 2020 (both gmx and
gmx_mpi) to see if my problem persists there or not...
If you're running on a single node, there's no need for an external MPI
library. Perhaps you've got a buggy implementation? Have you tried using
12 cores via the built-in thread MPI library?
-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.
Re: [gmx-users] [gmx-user] Autodock Vina Out use in gromacs MD
On 1/4/20 1:17 PM, Quin K wrote: Dear Proffesor Lemkul, I have given below the MD RMSD for complex, and noted that Ligand is getting detached again. When I viewed the trajectory on VMD it was confirmed. The ligand did not abruptly got dislodged instead it slowly came out of binding pocket and started moving around after. https://drive.google.com/file/d/1IBMU-8SzSgXVr_h9zyeVwNV7kQ4at8-S/view?usp=sharing It would be more useful to investigate which interactions are broken first or if there is a dihedral that rotates that leads to a conformational change in the ligand. RMSD tells you very little. I know that following CGenFF tutorial and fixing the molecule and reparameterization would be the correct thing to do however I lack time at this moment. I read the paper and went through the tutorial and it's some what of a complex method to fix the parameters. I was thinking if I should use a different force-field such as Gromos with parameterization with ATB server. I have already submitted the given molecule below for optimization in ATB and the parameterization is now complete. Other option is to use Amber force field. Kindly let me know what your opinion on this. The nice thing about CGenFF is it tells you where it thinks problems might be and how they score in terms of quality. Neither of the other options do that. You always need to validate a ligand topology. Black boxes might work well or they might work poorly. You just don't know. Molecule https://drive.google.com/file/d/1Ni8rUX4sH3aKaRhhXqCZr9w8VJVetCI7/view?usp=sharing Interactions at binding site us DS Visualizer https://drive.google.com/file/d/16EkWYDPDyTfkERiQgaOYo4XxYxqslOD0/view?usp=sharing Also please let me know if you think the given interactions are enough to keep the molecule at binding site for like 100ns? The Arg-ligand interaction should be pretty strong, but you have an identified "unfavorable" contact (which could be due to the rotameric state of Asn111 being suboptimal, and otherwise only nonpolar contacts. I wouldn't expect a very favorable binding free energy. -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.
Re: [gmx-users] Need help with installation of Gromacs-2019.3 with Intell compilers
Hi, As a work-around it is possible to put "#pragma intel optimization_level 2" in front pull_calc_coms in file src/gromacs/pulling/pullutil.cpp or use Intel compiler 2019u4 which doesn't have the problem. Lowering the optimization for the one function shouldn't have a significant impact on performance even if you use pulling because this function isn't compute intensive. A full fix is in the works. Roland > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > On Behalf Of Rajib > Biswas > Sent: Monday, December 30, 2019 6:13 AM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Need help with installation of Gromacs-2019.3 with > Intell compilers > > Dear Gromacs-Users, > > Is there any update on this issue? I have used the following flags for version > 2019.3 > > /apps/codes/cmake/3.15.4/bin/cmake .. > -DCMAKE_INSTALL_PREFIX=/opt/gromacs/2019.3 - > DGMX_FFT_LIBRARY=fftw3 > -DCMAKE_PREFIX_PATH=/apps/libs/fftw/3.3.8 -DBUILD_SHARED_LIBS=OFF > -DGMX_DOUBLE=ON -DGMX_SIMD=AVX2_256 - > DCMAKE_C_COMPILER=mpiicc -DCMAKE_CXX_COMPILER=mpiicpc - > DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_BUILD_MDRUN_ONLY=ON > > and getting compilation error which says: > > [ 58%] Building CXX object > src/gromacs/CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o > icpc: error #10105: > /apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom: > core dumped > icpc: warning #10102: unknown signal(-497903120) > icpc: error #10106: Fatal error in > /apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom, > terminated by unknown > compilation aborted for > /storage/rajib/opt/gromacs-2019.3/src/gromacs/pulling/pullutil.cpp (code 1) > make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o] > Error 1 > make[2]: *** Waiting for unfinished jobs > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2 > make: *** [all] Error 2 > > Your help will be highly appreciated. > > Thanking you. > > With regards, > Rajib > > > > On Wed, Oct 9, 2019 at 4:03 AM Lyudmyla Dorosh > wrote: > > > I have tried this command line: > > sudo cmake .. -DBUILD_SHARED_LIBS=OFF -DGMX_FFT_LIBRARY=mkl > > -DCMAKE_INSTALL_PREFIX=$installDir -DGMX_MPI=ON - > DGMX_OPENMP=ON > > -DGMX_CYCLE_SUBCOUNTERS=ON -DGMX_GPU=OFF -DGMX_SIMD=SSE2 > > -DCMAKE_C_COMPILER="/home/doroshl/apps/intel/bin/icc" > > -DCMAKE_CXX_COMPILER="/home/doroshl/apps/intel/bin/icpc" > > -DREGRESSIONTEST_DOWNLOAD=ON > > which had no errors for *cmake* or *make -j 4*, but *make check* gave > > me an > > error: > > ... > > [100%] Running all tests except physical validation Test project > > /home/doroshl/gromacs-2019.3/build > > Start 1: TestUtilsUnitTests > > 1/46 Test #1: TestUtilsUnitTests ..***Failed0.00 sec > > /home/doroshl/gromacs-2019.3/build/bin/testutils-test: error while > > loading shared libraries: libmkl_intel_lp64.so: cannot open shared > > object file: No such file or directory ... > > 0% tests passed, 46 tests failed out of 46 > > > > so I included libmkl_intel_lp64.so: > > sudo cmake .. -DBUILD_SHARED_LIBS=OFF -DGMX_FFT_LIBRARY=mkl > > -DCMAKE_INSTALL_PREFIX=$installDir > > > > - > DMKL_LIBRARIES="/home/doroshl/apps/intel/compilers_and_libraries_2019 > .5.281/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so" > > -DMKL_INCLUDE_DIR="/home/doroshl/apps/intel/intelpython2/lib" > > -DCMAKE_CXX_LINK_FLAGS="-Wl,-rpath,/usr/bin/gcc/lib64 - > L/usr/bin/gcc/lib64" > > -DGMX_MPI=ON -DGMX_OPENMP=ON - > DGMX_CYCLE_SUBCOUNTERS=ON -DGMX_GPU=OFF > > -DGMX_SIMD=SSE2 - > DCMAKE_C_COMPILER="/home/doroshl/apps/intel/bin/icc" > > -DCMAKE_CXX_COMPILER="/home/doroshl/apps/intel/bin/icpc" > > -DREGRESSIONTEST_DOWNLOAD=ON &> cmake.out which doesn't give > any error > > messages for cmake, but then in *sudo make -j > > 4 *results in > > > > [ 46%] Building CXX object > > src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o > > icpc: error #10105: > > > > > /home/doroshl/apps/intel/compilers_and_libraries_2019.5.281/linux/bin/int > el64/mcpcom: > > core dumped > > icpc: warning #10102: unknown signal(694380720) > > icpc: error #10106: Fatal error in > > > > /home/doroshl/apps/intel/compilers_and_libraries_2019.5.281/linux/bin/ > > intel64/mcpcom, > > terminated by unknown > > compilation aborted for > > /home/doroshl/gromacs-2019.3/src/gromacs/pulling/pullutil.cpp (code 1) > > src/gromacs/CMakeFiles/libgromacs.dir/build.make:2136: recipe for > > target 'src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o' > > failed > > make[2]: *** > > [src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o] > > Error 1 > > make[2]: *** Waiting for unfinished jobs > > CMakeFiles/Makefile2:2499: recipe for target > > 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed > > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2 > > Makefile:162: recipe for target 'all' failed > > make: *** [all] Error 2 > > Thanks for any help > > > > > > On Tue, Oct 8, 2019 at
[gmx-users] CMAP format on GROMCACS
Hi everybody! Happy new year! =) I would like to understand a little bit better the CMAP format of charmm27.ff within GROMACS. I've looked up in the manual but found little information. I understand that it is defined by 5 atoms (1-4 phi and 2-5 psi), a arbitrary identification number (e.g. 1) and the grid size (e.g. 24x24). But the following grid values are lines with just 10 values each, ended with a "\", instead of a 24 columns- 24 lines matrix. How are those values of CMAP formatted in GMX? Does GMX automatically transform those values in a matrix and, if so, can I consider that its "y-axis" would be PSI and "x-axis" would be PHI? Cheers! -- Marcelo Depólo Polêto Postdoctoral Researcher BIOAGRO - Room T07 Department of General Biology - UFV Contact: + 55 31 3612-2464 -- 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] atom moved too far
Justin, thank you.
I have implemented the pull code but that also exhibits the same error when
I use 12 cores (failed at about 2ns) and the simulation goes on fine when I
use 6 cores (now at about 32 ns).
I tried using the v-rescale thermostat (instead of Nose-Hoover) and
Parinello-Rahman barostat, which failed. I also tried the v-rescale
thermostat and the Berendsen barostat but that also failed. It seems to me
that this is not an equilibration issue.
So, to summarize, only if I decrease the time step to 0.001 ps or decrease
the number of cores seem to allow the calculation to proceed.
In this email list, I read that someone else was trying to use different
arguments supplied to mdrun (-nt, -ntomp etc) to solve the same problem. Is
it possible that the problem arises due to my running gmx_mpi on a single
node? This is the command I use in my submission script:
mpirun --mca btl tcp,sm,self /opt/gromacs-2018.1/bin/gmx_mpi mdrun -ntomp
\$ntomp -v -deffnm "${inputfile%.tpr}"
If you think that this is not due to a physics issue I can continue doing
calculations with 6 cores and try to install gromacs 2020 (both gmx and
gmx_mpi) to see if my problem persists there or not...
Best wishes,
Christos Deligkaris, PhD
On Thu, Jan 2, 2020 at 7:48 PM Justin Lemkul wrote:
>
>
> On 1/2/20 3:02 PM, Christos Deligkaris wrote:
> > thank you Justin.
> >
> > I saw on your umbrella sampling tutorial how to implement the restraints
> > using the pull code.
> >
> > The protocol I used is (if I understand correctly your question): The
> > energy minimization reached the cutoff for maximum force 1000 in 346
> steps.
> > My NVT equilibration was 50,000 steps of dt = 0.002 and I used 8 NPT
> > equilibration calculations, each with 31,250 steps of dt=0.002 (total NPT
> > equilibration time 500ps) where I slowly decreased the position
> restraints
> > on DNA and the small molecule, as well as the harmonic restraint between
> > the two.
> > What are the best temperature coupling groups to use when we are not
> > certain whether the small molecule will spend the entire simulation
> period
> > physically bound to the macromolecule or whether it will become fully
> > solvated at some point? Is Macromolecule and Non-macromolecule the best
> > option since the small molecule will always (to a small or large extent)
> > interact with water (versus the Macromolecule_and_small_molecule and
> > everything else grouping option)?
>
> I doubt there would be a measurable or provable difference between the
> behaviors of the two setups.
>
> -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.
[gmx-users] gmx covar error in gromacs2019.x
Hi gmx users! I am using gmx2019.4 in centos 7.6 (gcc version 4.8.5), the MD was conducted successfully. However, when I proceeded the PCA analysis, there was a wrong in the output informations. command: echo 3 3|gmx covar -f md_res_center_mol_fit_protein.xtc -s ../md.tpr -o eigenvalues.xvg -v eigenvectors.trr -xpma covapic.xpm -n ../index.ndx output: Choose a group for the least squares fit Group 0 (System) has 124748 elements Group 1 (Protein) has 8851 elements Group 2 ( Protein-H) has 4419 elements Group 3 (C-alpha) has 574 elements Group 4 ( Backbone) has 1722 elements Group 5 ( MainChain) has 2298 elements Group 6 ( MainChain+Cb) has 2824 elements Group 7 ( MainChain+H) has 2852 elements Group 8 ( SideChain) has 5999 elements Group 9 ( SideChain-H) has 2121 elements Group 10 ( Prot-Masses) has 8851 elements Group 11 ( non-Protein) has 115897 elements Group 12 ( Other) has 23 elements Group 13 ( MOL) has 23 elements Group 14 ( NA) has 8 elements Group 15 ( Water) has 115866 elements Group 16 ( SOL) has 115866 elements Group 17 ( non-Water) has 8882 elements Group 18 ( Ion) has 8 elements Group 19 ( MOL) has 23 elements Group 20 ( NA) has 8 elements Group 21 ( Water_and_ions) has 115874 elements Group 22 ( Protein_lig) has 8874 elements Group 23 (center_Val108_A) has 16 elements Group 24 (chain_A) has 4427 elements Group 25 (chain_B) has 4424 elements Group 26 (C-alpha__chain_A) has 287 elements Group 27 (C-alpha__chain_B) has 287 elements Group 28 ( E53) has 15 elements Group 29 ( K135) has 22 elements Group 30 ( C169) has 11 elements Group 31 ( S) has 1 elements Group 32 ( C13) has 1 elements Select a group: Selected 3: 'C-alpha' Choose a group for the covariance analysis Group 0 (System) has 124748 elements Group 1 (Protein) has 8851 elements Group 2 ( Protein-H) has 4419 elements Group 3 (C-alpha) has 574 elements Group 4 ( Backbone) has 1722 elements Group 5 ( MainChain) has 2298 elements Group 6 ( MainChain+Cb) has 2824 elements Group 7 ( MainChain+H) has 2852 elements Group 8 ( SideChain) has 5999 elements Group 9 ( SideChain-H) has 2121 elements Group 10 ( Prot-Masses) has 8851 elements Group 11 ( non-Protein) has 115897 elements Group 12 ( Other) has 23 elements Group 13 ( MOL) has 23 elements Group 14 ( NA) has 8 elements Group 15 ( Water) has 115866 elements Group 16 ( SOL) has 115866 elements Group 17 ( non-Water) has 8882 elements Group 18 ( Ion) has 8 elements Group 19 ( MOL) has 23 elements Group 20 ( NA) has 8 elements Group 21 ( Water_and_ions) has 115874 elements Group 22 ( Protein_lig) has 8874 elements Group 23 (center_Val108_A) has 16 elements Group 24 (chain_A) has 4427 elements Group 25 (chain_B) has 4424 elements Group 26 (C-alpha__chain_A) has 287 elements Group 27 (C-alpha__chain_B) has 287 elements Group 28 ( E53) has 15 elements Group 29 ( K135) has 22 elements Group 30 ( C169) has 11 elements Group 31 ( S) has 1 elements Group 32 ( C13) has 1 elements Select a group: Selected 3: 'C-alpha' Calculating the average structure ... Reading frame 0 time 0.000 WARNING: number of atoms in tpx (574) and trajectory (8851) do not match Last frame 1 time10.000 Back Off! I just backed up average.pdb to ./#average.pdb.3# Constructing covariance matrix (1722x1722) ... Last frame 1 time10.000 Read 10001 frames Trace of the covariance matrix: 9.58344 (nm^2) Back Off! I just backed up covapic.xpm to ./#covapic.xpm.3# 100% Diagonalizing ... --- Program: gmx covar, version 2019.4 Source file: src/gromacs/linearalgebra/eigensolver.cpp (line 137) Fatal error: Internal errror in LAPACK diagonalization. For more information and tips for troubleshooting, please check the GROMACS website athttp://www.gromacs.org/Documentation/Errors --- I had tested the same files in a virtual machine with centos 7.6 and gmx2019.4 installed, the output was normal and gave the output files I need. Then I used the same files on other server with gmx 4.5.3, and the md.tpr was replaced by md.gro, it was also normal. I had installed gmx2019.2, gmx2019.5 and it gave the same error. the gmx was installed as follows: cmake(version 3.16.0) tar xvf cmake-*.tar.gz cd cmake-* ./bootstrap gmake gmake install yum remove cmake -y ln -s /usr/local/bin/cmake /usr/bin/ fftw-3.3.8 tar -zxvf fftw* cd fftw* ./configure --prefix=/usr/local/fftw3.3.8 --enable-sse2 --enable-avx --enable-avx2 --enable-float --enable-shared make install -j 16 gmx2019.4 tar xfz gromacs-2019.4.tar.gz cd gromacs-2019.4 mkdir build cd build export
