Re: [gmx-users] Pull Code Error "unknown left hand"
Hi, take a look at the mdout.mdp grompp output file. There you should see how the pull-related parameters are called in the version you were using. Maybe you just need to use minus signs instead of the underlines. Best, Carsten > On 05 Oct 2015, at 04:25, Stella Nickerson wrote: > > I am attempting to pull a particle across a simulation box. I did it > several times with version 4.6.3 but this is my first attempting to do it > with version 5.0.4. > > I modified my mdp file for the new version based on the updated tutorial ( > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html). > My pull code looks like this: > > ; Pull code > pull= yes > pull_ngroups= 2 > pull_ncoords= 1 > pull_group1_name= DMY > pull_group2_name= DNP > pull_coord1_type= umbrella > pull_coord1_geometry= direction_periodic > pull_coord1_groups = 1 2 > pull_coord1_dim = N N Y > pull_coord1_rate= 0.01 > pull_coord1_k = 1000 > pull_start = yes > > I am getting an error message and several warnings. The error reads > "Invalid enum 'yes' for variable pull, using 'no' Next time use one of: > 'no' 'umbrella' 'constraint 'constant force.' > > The warnings read "unknown left-hand 'pull_ngroups' in parameter file", > with similar warnings for the other left-hand terms. > > I tried to compile a version using my old pull code from the earlier > version just to see what would happen and it gave fewer warnings, though it > didn't recognize "pull_vec1." So neither the old options nor the new > options work. > > I would love some clarification on this issue. > > Thanks, > > Stella Nickerson > -- > 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] PBC
Dear users, If I dont define pbc=no, what is the default type for gromacs? Is it right if I dont use pbc=no in my system while using grid for ns-type? thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] error unknown bond_atomtype CH1
After grompp command i got this error Fatal error unknown bond_atomtype CH1 Please help me solve his error thanks in advance Surbhi -- 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 unknown bond_atomtype CH1
Hi Surbhi, You are getting this error due to the Atomtype CH1 is not defined in your forcefield. Try to see if the CH1 is defined in atomtype.atp as well as ffbonded.itp On Mon, Oct 5, 2015 at 1:20 PM, surbhi mahajan wrote: > After grompp command i got this error > > Fatal error > unknown bond_atomtype CH1 > > Please help me solve his error > thanks in advance > > Surbhi > -- > 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] Energy minimization error
Thank you for your great help on specbond.dat file. I defined it and I could go ahead until Energy minimization step. I have used this minim.mdp file ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save 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 = 1; Frequency to update the neighbor list and long range forces ns_type = grid; Method to determine neighbor list (simple, grid) rlist = 1.0; Cut-off for making neighbor list (short range forces) 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) But when I run mdrun -v -deffnm em command, I get this error: Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 1000 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 90 steps, but did not reach the requested Fmax < 1000. Potential Energy = -2.3956744e+05 Maximum force = 1.5824519e+05 on atom 380 Norm of force = 1.7695243e+03 gcq#187: "Been There, Done It" (Beavis and Butthead) farideh@farideh-P61A-D3:~/FARIDEH$ I changed the emtol, emstep, and nsteps for a few times. However, I couldn't resolve this problem. Could you tell me if there is something wrong with the minim.mdp file? You can see all the files via: https://www.dropbox.com/s/sq2c103yxi4mc28/Farideh.zip?dl=0 Truly yours, Farideh -- 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] h-bonds by g_hbond and VMD and ptraj
Hi Erik, Thank you for fast reply. I knew about differences between definitions of angle criterion in Gromacs, VMD and cpptraj but I didn't realize that there is nontrivial relationship between these two different definitions. I have gone deeper into this problem and now it makes sence to me. Thank you. Ondřej Kroutil On Mon, Oct 5, 2015 at 1:07 AM, Erik Marklund wrote: > Hi Ondrej, > > They use different angles to determine if it is a bond or not. See > respective manuals. > > Kind regards, > Erik > > Erik Marklund, PhD > Postdoctoral Research Fellow > Fulford JRF, Somerville College > > Department of Chemistry > Physical & Theoretical Chemistry Laboratory > University of Oxford > South Parks Road > Oxford > OX1 3QZ > > > On 2 Oct 2015, at 16:39, Ondrej Kroutil wrote: > > > > Hi gromacs users. > > I did h-bond analysis between solute and solvent using g_hbond utility > with > > default settings (3.5A, 30°) and same analysis in VMD (Hydrogen bonds > > module) with same settings. And I get different numbers. So I did same > > analysis with cpptraj from Amber (angle 150° due to different definition > of > > h-bond angle criterion) and I get same results as in VMD (see table > below). > > Differences were even larger for distance 3.0A and angle 20°. So I tried > > different versions of Gromacs and results were same in all three > versions. > > > > nr. of h-bonds > > Grom (5.0), 3.5A, 30deg 9.343 > > Grom (5.0.5), 3.5A, 30deg 9.343 > > Grom (4.5.3), 3.5A, 30deg 9.343 > > VMD, 3.5A, 30deg 8.617 > > cpptraj, 3.5A, 150deg 8.617 > > > > Grom (5.0), 3.0A, 20deg 6.294 > > VMD, 3.0A, 20deg 4.317 > > cpptraj, 3.0A, 160deg 4.318 > > > > For g_hbond I used this command: > > > > g_hbond_gpu -s topol.tpr -f center-15.000.xtc -n index.ndx -a 30 -r 0.35 > > g_hbond_gpu -s topol.tpr -f center-15.000.xtc -n index.ndx -a 20 -r 0.30 > > > > Please, do you have any suggestions why I get different numbers from > > g_hbond compared to VMD and cpptraj??? > > > > Thank you very much and enjoy upcoming weekend. > > > > Ondrej Kroutil > > > > > > -- > > Ondřej Kroutil > >,, Faculty of Health and Social Studies > > "))' University of South Bohemia > > OOO Jirovcova 24, Ceske Budejovice > > OOO The Czech Republic > >| OO E-mail: okrou...@gmail.com > >> --O Mobile: +420 736 537 190 > > -- > > 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. -- Ondřej Kroutil ,, Faculty of Health and Social Studies "))' University of South Bohemia OOO Jirovcova 24, Ceske Budejovice OOO The Czech Republic | OO E-mail: okrou...@gmail.com >--O Mobile: +420 736 537 190 -- 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] coarse grained multi-body cut-off distance error
Dear Gromacs user, The coarse grained simulation was done by using the files prepared by the SMOG server. However, i got an error as follows: Not all bonded interactions have been properly assigned to the domain decomposition cells A list of missing interactions: LJ-14 of 2999 missing 1 Molecule type 'Macromolecule' the first 10 missing interactions, except for exclusions: LJ-14 atoms 370 1095 global 370 1095 --- Program mdrun, VERSION 4.5.4 Source code file: domdec_top.c, line: 356 Fatal error: 1 of the 16106 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (2 nm) or the two-body cut-off distance (2 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck The rlist value is 1.5 in .mdp file, and i give a value of 2 to -rdd, but i still got the problem. Please give me some information on the possible reason of the error. Best wishes Fugui -- 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] installing gromacs-5.0.5
Hello everybody; I want to install gromacs-5.0.5 in ubuntu-14.04 using the installation instruction in the website "gromacs.org", but in the "cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON" line I got this error: -- No compatible CUDA toolkit found (v4.0+), disabling native GPU acceleration CMake Error at cmake/gmxTestSimd.cmake:160 (message): Cannot find compiler flags for 128 bit AVX with FMA support. Use a newer compiler, or choose SSE4.1 SIMD (slower). Call Stack (most recent call first): CMakeLists.txt:720 (gmx_test_simd) -- Configuring incomplete, errors occurred! I've updated the gcc compiler but again this error occurred. I used the "sudo apt-get install gromacs" command but this installed the gromacs-4.6.5 and I want gromacs-5.0.5.can you help me, please? Thank you, Mohammad. -- 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] Building gromacs on CRAY XC40
Hi, Often the XC40 has a different kind of login vs compute node. Here it looks like you have configured for the compute node, but are actually using a toolchain to build for the login node. Use the Cray MPI wrapper compiler configured to use gcc as its back end as the compiler to give to CMake, and you should be fine. Mark On Mon, Oct 5, 2015 at 6:15 AM kevin chen wrote: > Dear Gromacs users, > > I am trying to build gromacs on our latest supercomputer CRAY XC40, but the > following errors using gcc and fftw. Here's my list of module loaded and > install script, can anyone give any instructions? > > = > Currently Loaded Modulefiles: > 1) modules/3.2.6.7 8) gcc/4.9.3 >15) xpmem/0.1-2.0502.55507.3.2.ari > 2) eswrap/1.1.0-1.020200.1231.0 9) cray-libsci/13.1.0 > 16) dvs/2.5_0.9.0-1.0502.1873.1.145.ari > 3) switch/1.0-1.0502.54233.2.96.ari 10) > udreg/2.3.2-1.0502.9275.1.12.ari 17) alps/5.2.1-2.0502.9041.11.6.ari > 4) craype-network-aries 11) ugni/5.0-1.0502.9685.4.24.ari >18) rca/1.0.0-2.0502.53711.3.127.ari > 5) craype/2.4.1 12) > pmi/5.0.8-1..10843.170.1.ari 19) atp/1.8.3 > 6) cray-mpich/7.2.4 13) > dmapp/7.0.1-1.0502.9501.5.219.ari20) PrgEnv-gnu/5.2.40 > 7) craype-ivybridge 14) > gni-headers/3.0-1.0502.9684.5.2.ari 21) fftw/3.3.4.4 > === > export CXX=`which cc` > export CC=`which cc` > export MPICC=`which cc` > export F77=`which ftn` > export INSTALL_PATH=/home1/03024/chenk/Software/Gromacs/install > > mkdir g_single_parallel > cd g_single_parallel > > > /home1/03024/chenk/Software/cmake/install/bin/cmake .. \ > -DCMAKE_INSTALL_PREFIX=$INSTALL_PATH \ > -DGMX_FFT_LIBRARY=fftw3 \ > -DGMX_X11=OFF \ > -DBUILD_SHARED_LIBS=OFF \ > -DGMX_PREFER_STATIC_LIBS=ON \ > -DGMX_BUILD_MDRUN_ONLY=OFF \ > -DGMX_MPI=ON -DGMX_OPENMP=ON \ > -DGMX_XML=OFF \ > -DGMX_SOFTWARE_INVSQRT=OFF \ > -DGMX_SKIP_DEFAULT_CFLAGS=ON \ > -DCMAKE_C_COMPILER=cc \ > -DCMAKE_C_FLAGS="-fomit-frame-pointer -finline-functions -funroll-all-loops > -O3 " \ > -DCMAKE_CXX_COMPILER=cc \ > -DCMAKE_CXX_FLAGS="-O3" \ > -DGMX_DEFAULT_SUFFIX=ON \ > -DGMX_EXTERNAL_BOOST=OFF \ > -DGMX_BUILD_SHARED_EXE=off > > make -j 12 > make install > = > Error messages: > > In file included from > > /opt/gcc/4.9.3/snos/lib/gcc/x86_64-suse-linux/4.9.3/include/immintrin.h:61:0, > from > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256.h:40, > from > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/simd.h:118, > from > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/gmxlib/bondfree.c:62: > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/simd_math.h: > In function 'gmx_simd_rsqrt_iter_f': > > /opt/gcc/4.9.3/snos/lib/gcc/x86_64-suse-linux/4.9.3/include/fmaintrin.h:159:1: > error: inlining failed in call to always_inline '_mm256_fnmadd_ps': target > specific option mismatch > _mm256_fnmadd_ps (__m256 __A, __m256 __B, __m256 __C) > ^ > In file included from > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/simd.h:118:0, > from > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/gmxlib/bondfree.c:62: > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256.h:61:36: > error: called from here > #define gmx_simd_fmadd_f _mm256_fmadd_ps > ^ > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/simd_math.h:146:12: > note: in expansion of macro 'gmx_simd_fmadd_f' > return gmx_simd_fmadd_f(gmx_simd_fnmadd_f(x, gmx_simd_mul_f(lu, lu), > gmx_simd_set1_f(1.0f)), gmx_simd_mul_f(lu, gmx_simd_set1_f(0.5f)), lu); > ^ > In file included from > > /opt/gcc/4.9.3/snos/lib/gcc/x86_64-suse-linux/4.9.3/include/immintrin.h:61:0, > from > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256.h:40, > from > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/simd.h:118, > from > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/gmxlib/bondfree.c:62: > > /opt/gcc/4.9.3/snos/lib/gcc/x86_64-suse-linux/4.9.3/include/fmaintrin.h:63:1: > error: inlining failed in call to always_inline '_mm256_fmadd_ps': target > specific option mismatch > _mm256_fmadd_ps (__m256 __A, __m256 __B, __m256 __C) > ^ > In file included from > > /home1/03024/chenk/Software/Gromacs/G
Re: [gmx-users] Energy minimization error
Hi, Look at atom 380 and see why the forces might be high. Mark On Mon, Oct 5, 2015 at 10:15 AM faride badalkhani wrote: > Thank you for your great help on specbond.dat file. I defined it and I > could go ahead until Energy minimization step. I have used this minim.mdp > file > > ; minim.mdp - used as input into grompp to generate em.tpr > ; Parameters describing what to do, when to stop and what to save > 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 = 1; Frequency to update the neighbor list and > long range forces > ns_type = grid; Method to determine neighbor list > (simple, grid) > rlist = 1.0; Cut-off for making neighbor list > (short range forces) > 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) > > But when I run mdrun -v -deffnm em command, I get this error: > > Energy minimization has stopped, but the forces have not converged to the > requested precision Fmax < 1000 (which may not be possible for your > system). > It stopped because the algorithm tried to make a new step whose size was > too > small, or there was no change in the energy since last step. Either way, we > regard the minimization as converged to within the available machine > precision, given your starting configuration and EM parameters. > > Double precision normally gives you higher accuracy, but this is often not > needed for preparing to run molecular dynamics. > You might need to increase your constraint accuracy, or turn > off constraints altogether (set constraints = none in mdp file) > > writing lowest energy coordinates. > > Steepest Descents converged to machine precision in 90 steps, > but did not reach the requested Fmax < 1000. > Potential Energy = -2.3956744e+05 > Maximum force = 1.5824519e+05 on atom 380 > Norm of force = 1.7695243e+03 > > gcq#187: "Been There, Done It" (Beavis and Butthead) > > farideh@farideh-P61A-D3:~/FARIDEH$ > > I changed the emtol, emstep, and nsteps for a few times. However, I > couldn't resolve this problem. Could you tell me if there is something > wrong with the minim.mdp file? > > You can see all the files via: > https://www.dropbox.com/s/sq2c103yxi4mc28/Farideh.zip?dl=0 > > Truly yours, > Farideh > -- > 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] PBC
Hi, See top of http://manual.gromacs.org/documentation/5.1/user-guide/mdp-options.html regarding defaults. Or you can leave it blank and inspect what gmx grompp writes to the mdout.mdp. Whether any PBC setting makes sense depends what you're trying to do, which we don't know. Mark On Mon, Oct 5, 2015 at 9:37 AM mah maz wrote: > Dear users, > > If I dont define pbc=no, what is the default type for gromacs? Is it right > if I dont use pbc=no in my system while using grid for ns-type? > > thank you. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Pull Code Error "unknown left hand"
Hi, Things change between versions when we recognize limitations of old decisions. 5.0 certainly recognizes pull-ngroups, so I think you were using a non-matching grompp at some point. You do have the option of reading the .mdp documentation for the version you're using. :-) (Of course, if it's out of date, let us know and we'll fix it!) Mark On Mon, Oct 5, 2015 at 9:10 AM Kutzner, Carsten wrote: > Hi, > > take a look at the mdout.mdp grompp output file. There you should see > how the pull-related parameters are called in the version you were using. > Maybe you just need to use minus signs instead of the underlines. > > Best, > Carsten > > > > On 05 Oct 2015, at 04:25, Stella Nickerson > wrote: > > > > I am attempting to pull a particle across a simulation box. I did it > > several times with version 4.6.3 but this is my first attempting to do it > > with version 5.0.4. > > > > I modified my mdp file for the new version based on the updated tutorial > ( > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html > ). > > My pull code looks like this: > > > > ; Pull code > > pull= yes > > pull_ngroups= 2 > > pull_ncoords= 1 > > pull_group1_name= DMY > > pull_group2_name= DNP > > pull_coord1_type= umbrella > > pull_coord1_geometry= direction_periodic > > pull_coord1_groups = 1 2 > > pull_coord1_dim = N N Y > > pull_coord1_rate= 0.01 > > pull_coord1_k = 1000 > > pull_start = yes > > > > I am getting an error message and several warnings. The error reads > > "Invalid enum 'yes' for variable pull, using 'no' Next time use one of: > > 'no' 'umbrella' 'constraint 'constant force.' > > > > The warnings read "unknown left-hand 'pull_ngroups' in parameter file", > > with similar warnings for the other left-hand terms. > > > > I tried to compile a version using my old pull code from the earlier > > version just to see what would happen and it gave fewer warnings, though > it > > didn't recognize "pull_vec1." So neither the old options nor the new > > options work. > > > > I would love some clarification on this issue. > > > > Thanks, > > > > Stella Nickerson > > -- > > 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] Hydrogen virtual sites and AMBER FF
IIRC, Mark Abraham wrote that there are some issues with implementation of vsites with amber ffs in GROMACS. Any more details? Is it possible to use amber99sb-ildn with -vsite option to speed up calculation? -- 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] Hydrogen virtual sites and AMBER FF
Hi, On Mon, Oct 5, 2015 at 12:49 PM Timofey Tyugashev wrote: > IIRC, Mark Abraham wrote that there are some issues with implementation > of vsites with amber ffs in GROMACS. > Shrug, that's meaningless without context. > Any more details? Is it possible to use amber99sb-ildn with -vsite > option to speed up calculation? > You can use vsites with AMBER force fields to use a larger time step. 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. > -- 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] PBC
Hi Mark, Thanks. It seems the default is pbc =xyz. But my question is if I don't use PBC, can I use grid, or grid is only meaningful when PBC is defined? On Mon, Oct 5, 2015 at 11:07 AM, mah maz wrote: > Dear users, > > If I dont define pbc=no, what is the default type for gromacs? Is it right > if I dont use pbc=no in my system while using grid for ns-type? > > thank you. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] genion problem
On 10/5/15 2:26 AM, Golnaz Roudsari wrote: Dear all I want to use bromide for neutralize my system. I wrote genion -s ions.tpr -c file.gro -p topol.top -pname K -nname BR -nn 24. After I cheked it the gromacs read Boron intead of bromide. I wrote command -nname BR -nn 24. and I did not use K but in all cases my output was boron and I did not see any Bromide. Something doesn't add up. But the only force field that supports Br- is OPLS-AA, so if you're using any other force field, whatever genion writes may not be correct or even supported by the force field. -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] PBC
Hi, I don't really remember. I suspect not, so I would look up the docs for ns-type, which should mention limitations, and otherwise try it out. grompp and/or mdrun are pretty good at complaining about things they can't do. Mark On Mon, Oct 5, 2015 at 12:56 PM mah maz wrote: > Hi Mark, > Thanks. It seems the default is pbc =xyz. But my question is if I don't use > PBC, can I use grid, or grid is only meaningful when PBC is defined? > > On Mon, Oct 5, 2015 at 11:07 AM, mah maz wrote: > > > Dear users, > > > > If I dont define pbc=no, what is the default type for gromacs? Is it > right > > if I dont use pbc=no in my system while using grid for ns-type? > > > > thank you. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools
Hi, That unfortunately doesn't tell us anything, since 1.5GB can still be read with 32-bit file operations. You didn't answer any of the questions: can you open very small xtc files, or very large (requiring 64-bit access) gro/pdb files, or not? We are still thinking that you should be able to open any files smaller than 2GB just fine, but you are making confusing claims that seem to contradict this, so this needs to be sorted out before we can really conclude anything. Best regards, Teemu On Mon, Oct 5, 2015, 08:32 Venkat Reddy wrote: > Hi, > Sorry for the delay in reply. > I am able to access pdb/gro files of size 1.5 GB with Gromacs-5.1 version. > My Desktop is 32-bit whereas my xtc files were generated on our super > cluster, which runs on 64-bit O.S. > > On Fri, Oct 2, 2015 at 9:46 AM, Teemu Murtola > wrote: > > > Hi, > > > > On Thu, Oct 1, 2015 at 6:30 PM Szilárd Páll > > wrote: > > > > > On Thu, Oct 1, 2015 at 8:01 AM, Venkat Reddy > > wrote: > > > > Gromacs-5.1 version can not read xtc files. However, it can access > > single > > > > frame gro/pdb files. > > > > > > > > > > That's a bold claim that IMO requires equally strong proof. > > > > > > > I agree with Szilard. Are you saying that you cannot even read a > > single-frame xtc file with just a few kB in size? How about other binary > > files (e.g., trr)? How about large (>2GB) gro files? > > > > In your other mail to the list you were talking about a 32-bit Ubuntu VM. > > > Are you sure you're not running into in incompatibility issue between > the > > > 32-bit binaries vs 64-bit xtc file(s) you're trying to read? > > > > > > > I would still suspect that the underlying reason is that for some reason, > > 5.1 gets compiled without large file support in your system, which makes > > even plain fopen() fail on large files. The build system should give an > > error if it cannot find 64-bit file support, but the check may be > > imperfect. Someone who can reproduce the issue (i.e., has access to a > > similar OS and other environment) should try what is actually required to > > get 64-bit file support working there. Based on the information you > posted > > in Redmine, the build system already checks that off_t is 64-bit without > > any extra defines on your system. The checks in the build system have not > > changed between 5.0 and 5.1, though. > > > > Teemu > > -- > > 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. > > > > > > -- > With Best Wishes > Venkat Reddy Chirasani > PhD student > Laboratory of Computational Biophysics > Department of Biotechnology > IIT Madras > Chennai > INDIA-600036 > -- > 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] Enthalpy of Vaporization
Hello Users, I need to calculate the cohesive energy for my system, for which the enthalpy of vaporization is needed. Am I right to assume that just the non-bonded interaction energy (potential energy) is required to calculate the enthalpy of vaporization ? Many Thanks! -Pallavi Banerjee -- 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] Enthalpy of Vaporization
On 10/5/15 10:53 AM, Pallavi Banerjee wrote: Hello Users, I need to calculate the cohesive energy for my system, for which the enthalpy of vaporization is needed. Am I right to assume that just the non-bonded interaction energy (potential energy) is required to calculate the enthalpy of vaporization ? No, that's only part of it. DHvap = - /Nmol + RT -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] Install Gromacs on VirtualBox
Oh, that was easy, should have asked about what the value of "GMX_SIMD" is in the CMake cache. Given that the GROMACS build system enabled AVX2 SIMD on your VM which seems to not support anything above SSE2, it's not a surprise that the first math instruction crashes the run. Immediate solution: set -DGMX_SIMD=SSE2 when configuring. Secondly: please open an issue on redmine.gromacs.org and briefly summarize what you described here (+ the VM setup you have) and attach the /proc/cpuinfo and CMakeCache.txt so we can have a look at why is the build system picking AVX2 even though the virtualized CPU does not support it. Thanks, -- Szilárd On Sun, Oct 4, 2015 at 4:04 AM, Simon Dürr wrote: > After running make check I can install via sudo make install. > gmx --version returns: > http://pastebin.com/Gnx09wah > > The CMakeCache file is the following: > http://pastebin.com/9wb0e1tw > > Cheers, > Simon > > 2015-10-02 17:58 GMT-04:00 Szilárd Páll : > > Should have asked for the CMakeCache file too, could you post that to a > > file sharing service? > > > > If you happen to have GMX_SIMD other than SSE2, that would explain the > > issue - although I can't imagine why would the instruction set detection > > fail. > > > > Do you get an "illegal instruction" error if you e.g. try to run "gmx > > -version" from the build tree? > > > > Cheers, > > > > -- > > Szilárd > > > > On Fri, Oct 2, 2015 at 11:12 PM, Simon Dürr > > > wrote: > > > >> Sure. > >> > >> >cat /proc/cpuinfo > >> > > >> > processor : 0 > >> > vendor_id : GenuineIntel > >> > cpu family : 6 > >> > model : 69 > >> > model name : Intel(R) Core(TM) i7-4550U CPU @ 1.50GHz > >> > stepping : 1 > >> > microcode : 0x19 > >> > cpu MHz : 2095.205 > >> > cache size : 6144 KB > >> > physical id : 0 > >> > siblings : 1 > >> > core id : 0 > >> > cpu cores : 1 > >> > apicid : 0 > >> > initial apicid : 0 > >> > fdiv_bug : no > >> > f00f_bug : no > >> > coma_bug : no > >> > fpu : yes > >> > fpu_exception : yes > >> > cpuid level : 5 > >> > wp : yes > >> > flags : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca cmov pat > >> pse36 clflush mmx fxsr sse sse2 rdtscp constant_tsc pni monitor ssse3 > >> > bugs : > >> > bogomips : 4190.41 > >> > clflush size : 64 > >> > cache_alignment : 64 > >> > address sizes : 39 bits physical, 48 bits virtual > >> > >> Cheers, > >> Simon > >> > >> 2015-10-02 5:36 GMT-04:00 Szilárd Páll : > >> > Hi, > >> > > >> > Can you share the CPUID flags shown in /proc/cpuinfo? > >> > > >> > > >> > -- > >> > Szilárd > >> > > >> > On Thu, Oct 1, 2015 at 7:03 PM, Simon Dürr < > simon.du...@uni-konstanz.de> > >> > wrote: > >> > > >> >> I used this: > >> >> > >> >> > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=OFF > >> >> -DGMX_USE_RDTSCP=OFF > >> >> > >> >> But Still: > >> >> Test project /home/simon/gromacs-5.0.6/build > >> >> Start 1: TestUtilsUnitTests > >> >> 1/15 Test #1: TestUtilsUnitTests ...***Exception: > >> >> Illegal 0.29 sec > >> >> > >> >> Start 2: PreprocessingTests > >> >> 2/15 Test #2: PreprocessingTests ...***Exception: > >> >> Illegal 0.23 sec > >> >> > >> >> Start 3: CommandLineUnitTests > >> >> 3/15 Test #3: CommandLineUnitTests .***Exception: > >> >> Illegal 0.36 sec > >> >> > >> >> Start 4: FFTUnitTests > >> >> 4/15 Test #4: FFTUnitTests .***Exception: > >> >> Illegal 0.32 sec > >> >> > >> >> Start 5: RandomUnitTests > >> >> 5/15 Test #5: RandomUnitTests ..***Exception: > >> >> Illegal 0.25 sec > >> >> > >> >> Start 6: OnlineHelpUnitTests > >> >> 6/15 Test #6: OnlineHelpUnitTests ..***Exception: > >> >> Illegal 0.30 sec > >> >> > >> >> Start 7: OptionsUnitTests > >> >> 7/15 Test #7: OptionsUnitTests .***Exception: > >> >> Illegal 0.31 sec > >> >> > >> >> Start 8: UtilityUnitTests > >> >> 8/15 Test #8: UtilityUnitTests .***Exception: > >> >> Illegal 0.26 sec > >> >> > >> >> Start 9: FileIOTests > >> >> 9/15 Test #9: FileIOTests ..***Exception: > >> >> Illegal 0.31 sec > >> >> > >> >> Start 10: SimdUnitTests > >> >> 10/15 Test #10: SimdUnitTests ***Exception: > >> >> Illegal 0.30 sec > >> >> > >> >> Start 11: LegacyToolsTests > >> >> 11/15 Test #11: LegacyToolsTests .***Exception: > >> >> Illegal 0.30 sec > >> >> > >> >> Start 12: AnalysisDataUnitTests > >> >> 12/15 Test #12: AnalysisDataUnitTests ***Exception: > >> >> Illegal 0.23 sec > >> >> > >> >> Start 13: SelectionUnitTests > >> >> 13/15 Test #13: SelectionUnitTests ...***Exception: > >> >> Illegal 0.35 sec > >> >> > >> >> Start 14: TrajectoryAnalysisUnitTests > >> >> 14/15 Test #14: TrajectoryAnalysisUnitTests ..***Exception: > >> >> Illegal 0.35 sec > >> >> > >> >> Start 15: MdrunTests > >> >> 15/15 Test #15: MdrunTests
Re: [gmx-users] Building gromacs on CRAY XC40
On Mon, Oct 5, 2015 at 6:15 AM, kevin chen wrote: > Dear Gromacs users, > > I am trying to build gromacs on our latest supercomputer CRAY XC40, but the > following errors using gcc and fftw. Here's my list of module loaded and > install script, can anyone give any instructions? > > = > Currently Loaded Modulefiles: > 1) modules/3.2.6.7 8) gcc/4.9.3 >15) xpmem/0.1-2.0502.55507.3.2.ari > 2) eswrap/1.1.0-1.020200.1231.0 9) cray-libsci/13.1.0 > 16) dvs/2.5_0.9.0-1.0502.1873.1.145.ari > 3) switch/1.0-1.0502.54233.2.96.ari 10) > udreg/2.3.2-1.0502.9275.1.12.ari 17) alps/5.2.1-2.0502.9041.11.6.ari > 4) craype-network-aries 11) ugni/5.0-1.0502.9685.4.24.ari >18) rca/1.0.0-2.0502.53711.3.127.ari > 5) craype/2.4.1 12) > pmi/5.0.8-1..10843.170.1.ari 19) atp/1.8.3 > 6) cray-mpich/7.2.4 13) > dmapp/7.0.1-1.0502.9501.5.219.ari20) PrgEnv-gnu/5.2.40 > 7) craype-ivybridge 14) > gni-headers/3.0-1.0502.9684.5.2.ari 21) fftw/3.3.4.4 > === > export CXX=`which cc` > export CC=`which cc` > export MPICC=`which cc` > export F77=`which ftn` > export INSTALL_PATH=/home1/03024/chenk/Software/Gromacs/install > > mkdir g_single_parallel > cd g_single_parallel > > > /home1/03024/chenk/Software/cmake/install/bin/cmake .. \ > -DCMAKE_INSTALL_PREFIX=$INSTALL_PATH \ > -DGMX_FFT_LIBRARY=fftw3 \ > -DGMX_X11=OFF \ > -DBUILD_SHARED_LIBS=OFF \ > -DGMX_PREFER_STATIC_LIBS=ON \ > -DGMX_BUILD_MDRUN_ONLY=OFF \ > -DGMX_MPI=ON -DGMX_OPENMP=ON \ > -DGMX_XML=OFF \ > -DGMX_SOFTWARE_INVSQRT=OFF \ > -DGMX_SKIP_DEFAULT_CFLAGS=ON \ > -DCMAKE_C_COMPILER=cc \ > -DCMAKE_C_FLAGS="-fomit-frame-pointer -finline-functions -funroll-all-loops > -O3 " \ > -DCMAKE_CXX_COMPILER=cc \ > -DCMAKE_CXX_FLAGS="-O3" \ > "cc" should typically be a Cray compiler wrapper, so Mark's guess about the compiler rather than the wrapper being using is likely not the reason for the errors. I think the issue is that you seem to want to override _all_ GROMACS default compiler flags (BTW, amy I ask why do you want to do that?). In any case, if you believe you have something that works better for you or you want to test flags, you're free to do that, but you can't omit essential flags. In this case you seem to be missing those that enable SIMD intrinsics, that is -mavx2 (or in some gcc versions that's not supported, so you need to use -march=core-avx2). AFAICT you're not adding any of those flags and that would explain why does your build fail to recognize SIMD instrinsics. Let me know if your issue is solved and it would be interesting to hear if found a combination of flags that gives better performance than our default ones! Cheers, -- Szilárd > -DGMX_DEFAULT_SUFFIX=ON \ > -DGMX_EXTERNAL_BOOST=OFF \ > -DGMX_BUILD_SHARED_EXE=off > > make -j 12 > make install > = > Error messages: > > In file included from > > /opt/gcc/4.9.3/snos/lib/gcc/x86_64-suse-linux/4.9.3/include/immintrin.h:61:0, > from > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256.h:40, > from > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/simd.h:118, > from > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/gmxlib/bondfree.c:62: > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/simd_math.h: > In function 'gmx_simd_rsqrt_iter_f': > > /opt/gcc/4.9.3/snos/lib/gcc/x86_64-suse-linux/4.9.3/include/fmaintrin.h:159:1: > error: inlining failed in call to always_inline '_mm256_fnmadd_ps': target > specific option mismatch > _mm256_fnmadd_ps (__m256 __A, __m256 __B, __m256 __C) > ^ > In file included from > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/simd.h:118:0, > from > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/gmxlib/bondfree.c:62: > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256.h:61:36: > error: called from here > #define gmx_simd_fmadd_f _mm256_fmadd_ps > ^ > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/simd_math.h:146:12: > note: in expansion of macro 'gmx_simd_fmadd_f' > return gmx_simd_fmadd_f(gmx_simd_fnmadd_f(x, gmx_simd_mul_f(lu, lu), > gmx_simd_set1_f(1.0f)), gmx_simd_mul_f(lu, gmx_simd_set1_f(0.5f)), lu); > ^ > In file included from > > /opt/gcc/4.9.3/snos/lib/gcc/x86_64-suse-linux/4.9.3/include/immintrin.h:61:0, > from > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5
Re: [gmx-users] Building gromacs on CRAY XC40
Hi, Indeed, although having the craype-ivybridge module loaded (when perhaps it was not loaded at CMake time) does not look like it would help. Mark On Mon, Oct 5, 2015 at 5:47 PM Szilárd Páll wrote: > On Mon, Oct 5, 2015 at 6:15 AM, kevin chen wrote: > > > Dear Gromacs users, > > > > I am trying to build gromacs on our latest supercomputer CRAY XC40, but > the > > following errors using gcc and fftw. Here's my list of module loaded and > > install script, can anyone give any instructions? > > > > = > > Currently Loaded Modulefiles: > > 1) modules/3.2.6.7 8) gcc/4.9.3 > >15) xpmem/0.1-2.0502.55507.3.2.ari > > 2) eswrap/1.1.0-1.020200.1231.0 9) cray-libsci/13.1.0 > > 16) dvs/2.5_0.9.0-1.0502.1873.1.145.ari > > 3) switch/1.0-1.0502.54233.2.96.ari 10) > > udreg/2.3.2-1.0502.9275.1.12.ari 17) alps/5.2.1-2.0502.9041.11.6.ari > > 4) craype-network-aries 11) > ugni/5.0-1.0502.9685.4.24.ari > >18) rca/1.0.0-2.0502.53711.3.127.ari > > 5) craype/2.4.1 12) > > pmi/5.0.8-1..10843.170.1.ari 19) atp/1.8.3 > > 6) cray-mpich/7.2.4 13) > > dmapp/7.0.1-1.0502.9501.5.219.ari20) PrgEnv-gnu/5.2.40 > > 7) craype-ivybridge 14) > > gni-headers/3.0-1.0502.9684.5.2.ari 21) fftw/3.3.4.4 > > > === > > export CXX=`which cc` > > export CC=`which cc` > > export MPICC=`which cc` > > export F77=`which ftn` > > export INSTALL_PATH=/home1/03024/chenk/Software/Gromacs/install > > > > mkdir g_single_parallel > > cd g_single_parallel > > > > > > /home1/03024/chenk/Software/cmake/install/bin/cmake .. \ > > -DCMAKE_INSTALL_PREFIX=$INSTALL_PATH \ > > -DGMX_FFT_LIBRARY=fftw3 \ > > -DGMX_X11=OFF \ > > -DBUILD_SHARED_LIBS=OFF \ > > -DGMX_PREFER_STATIC_LIBS=ON \ > > -DGMX_BUILD_MDRUN_ONLY=OFF \ > > -DGMX_MPI=ON -DGMX_OPENMP=ON \ > > -DGMX_XML=OFF \ > > -DGMX_SOFTWARE_INVSQRT=OFF \ > > -DGMX_SKIP_DEFAULT_CFLAGS=ON \ > > -DCMAKE_C_COMPILER=cc \ > > -DCMAKE_C_FLAGS="-fomit-frame-pointer -finline-functions > -funroll-all-loops > > -O3 " \ > > -DCMAKE_CXX_COMPILER=cc \ > > -DCMAKE_CXX_FLAGS="-O3" \ > > > > "cc" should typically be a Cray compiler wrapper, so Mark's guess about the > compiler rather than the wrapper being using is likely not the reason for > the errors. > > I think the issue is that you seem to want to override _all_ GROMACS > default compiler flags (BTW, amy I ask why do you want to do that?). In any > case, if you believe you have something that works better for you or you > want to test flags, you're free to do that, but you can't omit essential > flags. In this case you seem to be missing those that enable SIMD > intrinsics, that is -mavx2 (or in some gcc versions that's not supported, > so you need to use -march=core-avx2). > > AFAICT you're not adding any of those flags and that would explain why does > your build fail to recognize SIMD instrinsics. > > Let me know if your issue is solved and it would be interesting to hear if > found a combination of flags that gives better performance than our default > ones! > > Cheers, > -- > Szilárd > > > > > -DGMX_DEFAULT_SUFFIX=ON \ > > -DGMX_EXTERNAL_BOOST=OFF \ > > -DGMX_BUILD_SHARED_EXE=off > > > > make -j 12 > > make install > > = > > Error messages: > > > > In file included from > > > > > /opt/gcc/4.9.3/snos/lib/gcc/x86_64-suse-linux/4.9.3/include/immintrin.h:61:0, > > from > > > > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256.h:40, > > from > > > > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/simd.h:118, > > from > > > > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/gmxlib/bondfree.c:62: > > > > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/simd_math.h: > > In function 'gmx_simd_rsqrt_iter_f': > > > > > /opt/gcc/4.9.3/snos/lib/gcc/x86_64-suse-linux/4.9.3/include/fmaintrin.h:159:1: > > error: inlining failed in call to always_inline '_mm256_fnmadd_ps': > target > > specific option mismatch > > _mm256_fnmadd_ps (__m256 __A, __m256 __B, __m256 __C) > > ^ > > In file included from > > > > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/simd.h:118:0, > > from > > > > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/gmxlib/bondfree.c:62: > > > > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256.h:61:36: > > error: called from here > > #define gmx_simd_fmadd_f _mm256_fmadd_ps > > ^ > > > > > /home1/03024/chenk/Software/Gro
Re: [gmx-users] Enthalpy of Vaporization
This non-zero value becomes quite significant if you are dealing with highly flexible molecules - Internal molecular dynamics effects are different in the gas and liquid phases. Rasoul On Mon, Oct 5, 2015 at 3:53 PM, Pallavi Banerjee < pallavis...@students.iiserpune.ac.in> wrote: > Hello Users, > > I need to calculate the cohesive energy for my system, for which the > enthalpy of vaporization is needed. Am I right to assume that just the > non-bonded interaction energy (potential energy) is required to calculate > the enthalpy of vaporization ? > > Many Thanks! > > -Pallavi Banerjee > -- > 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] Enthalpy of Vaporization
Correct me if I am wrong, please. Ugas would be obtained from a simulation of a single molecule in vacuum. And U liq would be the total potential energy of the system (which is given by g_energy) minus the total bonded potential energy (bonds+angles+dihedrals). Am I thinking right? Thanks. -Pallavi Banerjee -- 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] Enthalpy of Vaporization
On 10/5/15 1:50 PM, Pallavi Banerjee wrote: Correct me if I am wrong, please. Ugas would be obtained from a simulation of a single molecule in vacuum. And U liq would be the total potential energy of the system (which is given by g_energy) minus the total bonded potential energy (bonds+angles+dihedrals). Am I thinking right? No. It's the actual potential energy. You need the whole potential energy to account for flexibility in the molecule. -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] Enthalpy of Vaporization
On Mon, Oct 5, 2015 at 6:52 PM, Justin Lemkul wrote: > > > On 10/5/15 1:50 PM, Pallavi Banerjee wrote: > >> Correct me if I am wrong, please. Ugas would be obtained from a simulation >> of a single molecule in vacuum. And U liq would be the total potential >> energy of the system (which is given by g_energy) minus the total bonded >> potential energy (bonds+angles+dihedrals). Am I thinking right? >> >> > No. It's the actual potential energy. You need the whole potential > energy to account for flexibility in the molecule. > > Hopefully FFs can do this because of the anharmonicity effects caused by multi-structural effects (e.g., many coupling of torsions). This scenario will be serious when T goes up. Rasoul == > -- > 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] Enthalpy of Vaporization
On 10/5/15 2:01 PM, Rasoul Nasiri wrote: On Mon, Oct 5, 2015 at 6:52 PM, Justin Lemkul wrote: On 10/5/15 1:50 PM, Pallavi Banerjee wrote: Correct me if I am wrong, please. Ugas would be obtained from a simulation of a single molecule in vacuum. And U liq would be the total potential energy of the system (which is given by g_energy) minus the total bonded potential energy (bonds+angles+dihedrals). Am I thinking right? No. It's the actual potential energy. You need the whole potential energy to account for flexibility in the molecule. Hopefully FFs can do this because of the anharmonicity effects caused by multi-structural effects (e.g., many coupling of torsions). This scenario will be serious when T goes up. Indeed it depends to some extent on the size, flexibility, and chemical composition of the molecule. Additive FFs will inherently overestimate dipole moments to account for a lack of polarization response, so generally very polar molecules have poor DHvap values with additive models. Simple hydrophobics are easier and often agree better with experimental data. -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] Enthalpy of Vaporization
On Mon, Oct 5, 2015 at 7:03 PM, Justin Lemkul wrote: > > > On 10/5/15 2:01 PM, Rasoul Nasiri wrote: > >> On Mon, Oct 5, 2015 at 6:52 PM, Justin Lemkul wrote: >> >> >>> >>> On 10/5/15 1:50 PM, Pallavi Banerjee wrote: >>> >>> Correct me if I am wrong, please. Ugas would be obtained from a simulation of a single molecule in vacuum. And U liq would be the total potential energy of the system (which is given by g_energy) minus the total bonded potential energy (bonds+angles+dihedrals). Am I thinking right? No. It's the actual potential energy. You need the whole potential >>> energy to account for flexibility in the molecule. >>> >>> >>> Hopefully FFs can do this because of the anharmonicity effects caused by >> multi-structural effects (e.g., many coupling of torsions). This >> scenario will be serious when T goes up. >> >> > Indeed it depends to some extent on the size, flexibility, and chemical > composition of the molecule. Additive FFs will inherently overestimate > dipole moments to account for a lack of polarization response, so generally > very polar molecules have poor DHvap values with additive models. Simple > hydrophobics are easier and often agree better with experimental data. > It's even complex behaviour for long chain apolar molecules as there are many possibility for taken into account the coupling effects (rot, vib, conf and so on) especially at high T. Rasoul > -- > 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] RMSF calculation of carbon alpha
Hi there, I want to calculate ht RMSF of the carbon alpha. First which atoms are used if I calculate the RMSF per residue with -res and how can I calculate the RMSF of carbon alpha or NH vector etc? Can’t seem to find an input except for the group of the alignment for the -fit Thank you, Max -- 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] Building gromacs on CRAY XC40
On Mon, Oct 5, 2015 at 5:52 PM, Mark Abraham wrote: > Hi, > > Indeed, although having the craype-ivybridge module loaded (when perhaps it > was not loaded at CMake time) does not look like it would help. > That certainly does not look right (either), if the target is AVX2 (and AFAIK XC40 means HSW-E CPUs), than the craype-haswell module should be loaded. -- Szilárd > > Mark > > On Mon, Oct 5, 2015 at 5:47 PM Szilárd Páll > wrote: > > > On Mon, Oct 5, 2015 at 6:15 AM, kevin chen wrote: > > > > > Dear Gromacs users, > > > > > > I am trying to build gromacs on our latest supercomputer CRAY XC40, but > > the > > > following errors using gcc and fftw. Here's my list of module loaded > and > > > install script, can anyone give any instructions? > > > > > > > = > > > Currently Loaded Modulefiles: > > > 1) modules/3.2.6.7 8) gcc/4.9.3 > > >15) xpmem/0.1-2.0502.55507.3.2.ari > > > 2) eswrap/1.1.0-1.020200.1231.0 9) cray-libsci/13.1.0 > > > 16) dvs/2.5_0.9.0-1.0502.1873.1.145.ari > > > 3) switch/1.0-1.0502.54233.2.96.ari 10) > > > udreg/2.3.2-1.0502.9275.1.12.ari 17) > alps/5.2.1-2.0502.9041.11.6.ari > > > 4) craype-network-aries 11) > > ugni/5.0-1.0502.9685.4.24.ari > > >18) rca/1.0.0-2.0502.53711.3.127.ari > > > 5) craype/2.4.1 12) > > > pmi/5.0.8-1..10843.170.1.ari 19) atp/1.8.3 > > > 6) cray-mpich/7.2.4 13) > > > dmapp/7.0.1-1.0502.9501.5.219.ari20) PrgEnv-gnu/5.2.40 > > > 7) craype-ivybridge 14) > > > gni-headers/3.0-1.0502.9684.5.2.ari 21) fftw/3.3.4.4 > > > > > > === > > > export CXX=`which cc` > > > export CC=`which cc` > > > export MPICC=`which cc` > > > export F77=`which ftn` > > > export INSTALL_PATH=/home1/03024/chenk/Software/Gromacs/install > > > > > > mkdir g_single_parallel > > > cd g_single_parallel > > > > > > > > > /home1/03024/chenk/Software/cmake/install/bin/cmake .. \ > > > -DCMAKE_INSTALL_PREFIX=$INSTALL_PATH \ > > > -DGMX_FFT_LIBRARY=fftw3 \ > > > -DGMX_X11=OFF \ > > > -DBUILD_SHARED_LIBS=OFF \ > > > -DGMX_PREFER_STATIC_LIBS=ON \ > > > -DGMX_BUILD_MDRUN_ONLY=OFF \ > > > -DGMX_MPI=ON -DGMX_OPENMP=ON \ > > > -DGMX_XML=OFF \ > > > -DGMX_SOFTWARE_INVSQRT=OFF \ > > > -DGMX_SKIP_DEFAULT_CFLAGS=ON \ > > > -DCMAKE_C_COMPILER=cc \ > > > -DCMAKE_C_FLAGS="-fomit-frame-pointer -finline-functions > > -funroll-all-loops > > > -O3 " \ > > > -DCMAKE_CXX_COMPILER=cc \ > > > -DCMAKE_CXX_FLAGS="-O3" \ > > > > > > > "cc" should typically be a Cray compiler wrapper, so Mark's guess about > the > > compiler rather than the wrapper being using is likely not the reason for > > the errors. > > > > I think the issue is that you seem to want to override _all_ GROMACS > > default compiler flags (BTW, amy I ask why do you want to do that?). In > any > > case, if you believe you have something that works better for you or you > > want to test flags, you're free to do that, but you can't omit essential > > flags. In this case you seem to be missing those that enable SIMD > > intrinsics, that is -mavx2 (or in some gcc versions that's not supported, > > so you need to use -march=core-avx2). > > > > AFAICT you're not adding any of those flags and that would explain why > does > > your build fail to recognize SIMD instrinsics. > > > > Let me know if your issue is solved and it would be interesting to hear > if > > found a combination of flags that gives better performance than our > default > > ones! > > > > Cheers, > > -- > > Szilárd > > > > > > > > > -DGMX_DEFAULT_SUFFIX=ON \ > > > -DGMX_EXTERNAL_BOOST=OFF \ > > > -DGMX_BUILD_SHARED_EXE=off > > > > > > make -j 12 > > > make install > > > > = > > > Error messages: > > > > > > In file included from > > > > > > > > > /opt/gcc/4.9.3/snos/lib/gcc/x86_64-suse-linux/4.9.3/include/immintrin.h:61:0, > > > from > > > > > > > > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256.h:40, > > > from > > > > > > > > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/simd.h:118, > > > from > > > > > > > > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/gmxlib/bondfree.c:62: > > > > > > > > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/simd_math.h: > > > In function 'gmx_simd_rsqrt_iter_f': > > > > > > > > > /opt/gcc/4.9.3/snos/lib/gcc/x86_64-suse-linux/4.9.3/include/fmaintrin.h:159:1: > > > error: inlining failed in call to always_inline '_mm256_fnmadd_ps': > > target > > > specific option mismatch > > > _mm256_fnmadd_ps (__m256 __A, __m256 __B, __m256 __C) > > > ^ > > > In file included from > > > > > > > >
Re: [gmx-users] RMSF calculation of carbon alpha
I think I can answer my own question again. The group you use for root mean square calculation is also the RMSF group. If the group has more than one atom per residue and I use -res I get the average RMSF of all atoms per residue. Hope this is correct. Max > On Oct 5, 2015, at 2:46 PM, Ebert Maximilian wrote: > > Hi there, > > I want to calculate ht RMSF of the carbon alpha. First which atoms are used > if I calculate the RMSF per residue with -res and how can I calculate the > RMSF of carbon alpha or NH vector etc? Can’t seem to find an input except for > the group of the alignment for the -fit > > Thank you, > > Max > -- > 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] RMSF calculation of carbon alpha
Oh infact no thats not the case it is still the RMSF of all atoms in the residue. So back to my initial question. How can I calculate the RMSF on the Ca of each residue? Sorry if this caused any confusion. Max > On Oct 5, 2015, at 4:36 PM, Ebert Maximilian wrote: > > I think I can answer my own question again. The group you use for root mean > square calculation is also the RMSF group. If the group has more than one > atom per residue and I use -res I get the average RMSF of all atoms per > residue. > > Hope this is correct. > > Max > >> On Oct 5, 2015, at 2:46 PM, Ebert Maximilian wrote: >> >> Hi there, >> >> I want to calculate ht RMSF of the carbon alpha. First which atoms are used >> if I calculate the RMSF per residue with -res and how can I calculate the >> RMSF of carbon alpha or NH vector etc? Can’t seem to find an input except >> for the group of the alignment for the -fit >> >> Thank you, >> >> Max >> -- >> 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] RMSF calculation of carbon alpha
Hi Ebert, Use C-alpha as the group. Yes, it will be used for fitting and calculation of the RMSF. Cheers, Tsjerk On Oct 5, 2015 22:44, "Ebert Maximilian" wrote: > Oh infact no thats not the case it is still the RMSF of all atoms in the > residue. So back to my initial question. How can I calculate the RMSF on > the Ca of each residue? > > Sorry if this caused any confusion. > > Max > > > On Oct 5, 2015, at 4:36 PM, Ebert Maximilian > wrote: > > > > I think I can answer my own question again. The group you use for root > mean square calculation is also the RMSF group. If the group has more than > one atom per residue and I use -res I get the average RMSF of all atoms per > residue. > > > > Hope this is correct. > > > > Max > > > >> On Oct 5, 2015, at 2:46 PM, Ebert Maximilian > wrote: > >> > >> Hi there, > >> > >> I want to calculate ht RMSF of the carbon alpha. First which atoms are > used if I calculate the RMSF per residue with -res and how can I calculate > the RMSF of carbon alpha or NH vector etc? Can’t seem to find an input > except for the group of the alignment for the -fit > >> > >> Thank you, > >> > >> Max > >> -- > >> 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. -- 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] RMSF calculation of carbon alpha
Thanks for the clarification Tsjerk. So my previous assumption was right. Basically if I want to align on the backbone but want the RMSF of Calpha I need to align first, save the trajectory and do RMSF with -nofit right? Max > On Oct 5, 2015, at 4:54 PM, Tsjerk Wassenaar wrote: > > Hi Ebert, > > Use C-alpha as the group. Yes, it will be used for fitting and calculation > of the RMSF. > > Cheers, > > Tsjerk > On Oct 5, 2015 22:44, "Ebert Maximilian" wrote: > >> Oh infact no thats not the case it is still the RMSF of all atoms in the >> residue. So back to my initial question. How can I calculate the RMSF on >> the Ca of each residue? >> >> Sorry if this caused any confusion. >> >> Max >> >>> On Oct 5, 2015, at 4:36 PM, Ebert Maximilian >> wrote: >>> >>> I think I can answer my own question again. The group you use for root >> mean square calculation is also the RMSF group. If the group has more than >> one atom per residue and I use -res I get the average RMSF of all atoms per >> residue. >>> >>> Hope this is correct. >>> >>> Max >>> On Oct 5, 2015, at 2:46 PM, Ebert Maximilian >> wrote: Hi there, I want to calculate ht RMSF of the carbon alpha. First which atoms are >> used if I calculate the RMSF per residue with -res and how can I calculate >> the RMSF of carbon alpha or NH vector etc? Can’t seem to find an input >> except for the group of the alignment for the -fit Thank you, Max -- 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. > -- > 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] Free Energy of Liquid Water
Thank you, Professor Farais de Moura. That method of integrating to an ideal gas makes sense. However, I'm having trouble figuring out how to deal with the temperature. I hope my question isn't too basic, but I can't find any examples online and I know I am misunderstanding how it works. I want to integrate from about 200K to 1000K or so (above the critical temperature, which I believe is somewhere in the 700's of Kelvin for TIP4P water). To do this, I thought I would set the reference temperature to 1000, and increment temperature-lambda from 0.2 to 1, thinking that temperature-lambda would scale the absolute temperature. But after running a the simulations, it's evident that temperature-lambda does not affect the thermostat. Should I set the reference temperature to different temperatures for each run? What does the temperature-lambda affect in that case? Thanks for your help! Regards, Nathan H. - Original Message - From: "André Farias de Moura" To: "Discussion list for GROMACS users" Sent: Friday, October 2, 2015 9:26:28 AM Subject: Re: [gmx-users] Free Energy of Liquid Water Apart from stability/convergence issues, I guess that turning off all intermolecular interactions should take you to the ideal gas straightforwardly, but in a different (P,T) point as compared to your target. But if you managed to alchemically turn water into an ideal gas, then you just need to apply standard free change for an ideal gas along a (P,T) process to achieve your target state. (I have not found the reference, but I read a paper doing just that with Monte Carlo simulations a few years ago) you should be able to track the conversion of water into an ideal gas by means of the g(r) profiles, which should change from the typical TIP4P profiles to g(r)=1 for all distances ranging from zero to half of the smallest box length. On Thu, Oct 1, 2015 at 11:44 PM, Nathan K Houtz wrote: > Hi everyone, > > I would like to use Gromacs to do Thermodynamic Integration (TI) from > liquid water (TIP4P model) to an ideal gas, to find the relative free > energy. To do this, I believe one generally integrates above the critical > point by increasing the temperature above the critical temperature and then > relaxing the pressure until the system is a diffuse gas. The mdp options > documentation is helpful, and I went through an ethanol solvation tutorial, > but there doesn't appear to be a "pressure-lambda" or a "volume-lambda" > option that I could use to do the second part. How can I get Gromacs to > calculate the dh/dl derivative while relaxing the pressure? > > In addition, all of the tutorials I found for thermodynamic integration > were for finding solvation free energies. The coulomb and VDW forces are > essentially changed from "completely on" to "completely off". But in my > case, I'd like to change the temperature and pressure between two nonzero > values. I don't want to begin my simulation at 0K and 0atm, but lambda > *must* go from 0 to 1. How can I define both starting and ending points for > the temperature and pressure (or volume, or density)? > > Thanks for your help! > Nathan H. > -- > 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. > -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- 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] Enthalpy of Vaporization
My system is one molecule of Propanamide. I need to see if my force field makes the molecule water soluble or not, for which I would need its cohesive energy, and this in turn would require the heat of vaporization. So, I should include the total potential energy for both gas and liquid phase in the following calculation : (U gas - U liq) / Nmol + RT. Is that right? Thanks -Pallavi Banerjee -- 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] Analysis of old xtc file using gromacs-5 tools
Hi, Sorry for the confusion. Now I have generated a small xtc file and a very big pdb file. I can able to access small xtc file but unable to read the large pdb file (~10GB) (terminating with the same error as reported earlier). Does it mean my installation has some problem? On Mon, Oct 5, 2015 at 7:41 PM, Teemu Murtola wrote: > Hi, > > That unfortunately doesn't tell us anything, since 1.5GB can still be read > with 32-bit file operations. You didn't answer any of the questions: can > you open very small xtc files, or very large (requiring 64-bit access) > gro/pdb files, or not? We are still thinking that you should be able to > open any files smaller than 2GB just fine, but you are making confusing > claims that seem to contradict this, so this needs to be sorted out before > we can really conclude anything. > > Best regards, > Teemu > > On Mon, Oct 5, 2015, 08:32 Venkat Reddy wrote: > > > Hi, > > Sorry for the delay in reply. > > I am able to access pdb/gro files of size 1.5 GB with Gromacs-5.1 > version. > > My Desktop is 32-bit whereas my xtc files were generated on our super > > cluster, which runs on 64-bit O.S. > > > > On Fri, Oct 2, 2015 at 9:46 AM, Teemu Murtola > > wrote: > > > > > Hi, > > > > > > On Thu, Oct 1, 2015 at 6:30 PM Szilárd Páll > > > wrote: > > > > > > > On Thu, Oct 1, 2015 at 8:01 AM, Venkat Reddy > > > wrote: > > > > > Gromacs-5.1 version can not read xtc files. However, it can access > > > single > > > > > frame gro/pdb files. > > > > > > > > > > > > > That's a bold claim that IMO requires equally strong proof. > > > > > > > > > > I agree with Szilard. Are you saying that you cannot even read a > > > single-frame xtc file with just a few kB in size? How about other > binary > > > files (e.g., trr)? How about large (>2GB) gro files? > > > > > > In your other mail to the list you were talking about a 32-bit Ubuntu > VM. > > > > Are you sure you're not running into in incompatibility issue between > > the > > > > 32-bit binaries vs 64-bit xtc file(s) you're trying to read? > > > > > > > > > > I would still suspect that the underlying reason is that for some > reason, > > > 5.1 gets compiled without large file support in your system, which > makes > > > even plain fopen() fail on large files. The build system should give an > > > error if it cannot find 64-bit file support, but the check may be > > > imperfect. Someone who can reproduce the issue (i.e., has access to a > > > similar OS and other environment) should try what is actually required > to > > > get 64-bit file support working there. Based on the information you > > posted > > > in Redmine, the build system already checks that off_t is 64-bit > without > > > any extra defines on your system. The checks in the build system have > not > > > changed between 5.0 and 5.1, though. > > > > > > Teemu > > > -- > > > 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. > > > > > > > > > > > -- > > With Best Wishes > > Venkat Reddy Chirasani > > PhD student > > Laboratory of Computational Biophysics > > Department of Biotechnology > > IIT Madras > > Chennai > > INDIA-600036 > > -- > > 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. > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] (no subject)
GROMACS users, I was trying to perform a MD simulation of a system with a protein with Ag+ metal ion but realized that GROMACS does not have parameters for the Ag+ ion. I tried to include the parameters in the ion.itp file but did not succeed yet. Does anyone knows the right procedure to introduce this ions into the file ions.itp? do we have to change anything more in order to GROMACS recognize the new ion? *With Regards,* *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- 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
GROMACS users, I was trying to perform a MD simulation of a system with a protein with Ag+ metal ion but realized that GROMACS does not have parameters for the Ag+ ion. I tried to include the parameters in the ion.itp file but did not succeed yet. Does anyone knows the right procedure to introduce this ions into the file ions.itp? do we have to change anything more in order to GROMACS recognize the new ion? With Regards *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- 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] RMSF calculation of carbon alpha
Right :) Cheers, Tsjerk On Mon, Oct 5, 2015 at 11:07 PM, Ebert Maximilian wrote: > Thanks for the clarification Tsjerk. So my previous assumption was right. > Basically if I want to align on the backbone but want the RMSF of Calpha I > need to align first, save the trajectory and do RMSF with -nofit right? > > Max > > > On Oct 5, 2015, at 4:54 PM, Tsjerk Wassenaar wrote: > > > > Hi Ebert, > > > > Use C-alpha as the group. Yes, it will be used for fitting and > calculation > > of the RMSF. > > > > Cheers, > > > > Tsjerk > > On Oct 5, 2015 22:44, "Ebert Maximilian" wrote: > > > >> Oh infact no thats not the case it is still the RMSF of all atoms in the > >> residue. So back to my initial question. How can I calculate the RMSF on > >> the Ca of each residue? > >> > >> Sorry if this caused any confusion. > >> > >> Max > >> > >>> On Oct 5, 2015, at 4:36 PM, Ebert Maximilian > >> wrote: > >>> > >>> I think I can answer my own question again. The group you use for root > >> mean square calculation is also the RMSF group. If the group has more > than > >> one atom per residue and I use -res I get the average RMSF of all atoms > per > >> residue. > >>> > >>> Hope this is correct. > >>> > >>> Max > >>> > On Oct 5, 2015, at 2:46 PM, Ebert Maximilian > >> wrote: > > Hi there, > > I want to calculate ht RMSF of the carbon alpha. First which atoms are > >> used if I calculate the RMSF per residue with -res and how can I > calculate > >> the RMSF of carbon alpha or NH vector etc? Can’t seem to find an input > >> except for the group of the alignment for the -fit > > Thank you, > > Max > -- > 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. > > -- > > 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. > -- Tsjerk A. Wassenaar, Ph.D. -- 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.
