[gmx-users] Message-ID: Content-Type: text/plain; charset=UTF-8
Hey Mark, I tried to set the CMAKE_LIBRARY_PATH to an actual file, because it cannot be found by cmake if I left it out, but it is there. Greetings Kim > > Ursprüngliche Nachricht: > > Von: Kim Jessica Novacek > > An: gromacs.org_gmx-users@maillist.sys.kth.se > > Kopie: > > Datum: Mon Oct 12 15:31:58 CEST 2015 > > > > Although I did let out the Xeon Phi Command there is still the same make > > error. > > Greetings > > Kim > > > > > > /usr/bin/ld: cannot find -lcudart > > /usr/bin/ld: cannot find -lmpi > > collect2: error: ld returned 1 exit status > > make[2]: *** [bin/gmx_mpi] Fehler 1 > > make[1]: *** [src/programs/CMakeFiles/gmx.dir/all] Fehler 2 > > make[1]: *** Auf noch nicht beendete Prozesse wird gewartet … > > /usr/bin/ld: cannot find -lcudart > > /usr/bin/ld: cannot find -lmpi > > collect2: error: ld returned 1 exit status > > make[2]: *** [bin/template] Fehler 1 > > make[1]: *** [share/template/CMakeFiles/template.dir/all] Fehler 2 > > make: *** [all] Fehler 2 > > > > > > cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_C_COMPILER=/usr/bin/gcc > > -DGMX_MPI=ON > > -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit > > -DCMAKE_INSTALL_PREFIX=/usr > /l > > ocal/GROMACS -DGMX_FFT_LIBRARY=fftw3 > > -DFFTWF_LIBRARY=/usr/local/lib/libfftw3f.a > -DCMAKE_BUILD_T > > YPE=DEBUG -DCMAKE_CXX_COMPILER=/usr/bin/gcc -DGMX_PREFER_STATIC_LIBS=ON > > -DCMAKE_C_FLAGS="-sta > ti > > c" -DCMAKE_CXX_FLAGS="-static" -DCMAKE_SKIP_RPATH=YES > > -DCMAKE_PREFIX_PATH=/usr/lib/cuda > > -DCMAKE_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu/libcudart.so > > -DCMAKE_PREFIX_PATH=/usr/include/ > li > > bxml2/libxml > -- 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] Energy minimization error
Hi, What some visualization program shows about bonds doesn't mean anything - it has not parsed your topology. You have no option but to look at the .top produced and reason about what it shows, but yours is very complex. I strongly recommend starting with something simpler than a multiply branched dendrimer. Join two units with a specbond, inspect the .top so that you know it has what you think it has, and get that to EM and simulation stably. Then you can get more complex. Mark On Sat, Oct 17, 2015 at 3:58 PM faride badalkhani wrote: > Dear gromacs users, > > As I said before I faced with the minimization error, so I changed > coordinates of atoms in pdb file, but the problem is the same. the only > thing that changes in every run is atom number. I modified pdb for many > times. > > Steepest Descents converged to Fmax < 1000 in 530 steps > Potential Energy = -5.5180181e+05 > Maximum force = 7.4496063e+02 on atom 501 > Norm of force = 3.8248455e+01 > > > Moreover gro structure was completely messed up when was visualized in vmd. > you can see the picture of my structure in below dropbox link: > > https://www.dropbox.com/s/78v2cvii4gkd8ev/gro.bmp?dl=0 > https://www.dropbox.com/s/nyzyu3zmy1vvevg/pdb.bmp?dl=0 > > and this is the pdb file dropbox link: > > https://www.dropbox.com/s/yvxpl2igzi5ccad/120.pdb?dl=0 > > > I used cg algorithm after steep for minimization, too. But it did not work. > is there any way to solve this problem? > > any help is appreciated. > > On Mon, Oct 5, 2015 at 2:08 PM, Mark Abraham > wrote: > > > 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 < > > farideh.kham...@gmail.com> > > 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.grom
[gmx-users] constraining charges
Hi All, I have some amino-acid residue in which some extra side chain(s) attached by replacing H from amino-acid. I want to simulate this with CHARMM ff. Somehow I can choose best bonded params. But in order to keep integral charge on this modified aminoacid I was thinking if there is any way to derive charges of the side chain whose formal charge (net partial charge) be equal and opposite to net charge on amino-acid with removed Hydrogen. I saw Cgenff is available but it can not constrain some net charge and some times it does not work because of some non-acceptable functional groups or bonds. Please suggest, Thanks Jiom -- 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] Energy minimization error
Dear gromacs users, As I said before I faced with the minimization error, so I changed coordinates of atoms in pdb file, but the problem is the same. the only thing that changes in every run is atom number. I modified pdb for many times. Steepest Descents converged to Fmax < 1000 in 530 steps Potential Energy = -5.5180181e+05 Maximum force = 7.4496063e+02 on atom 501 Norm of force = 3.8248455e+01 Moreover gro structure was completely messed up when was visualized in vmd. you can see the picture of my structure in below dropbox link: https://www.dropbox.com/s/78v2cvii4gkd8ev/gro.bmp?dl=0 https://www.dropbox.com/s/nyzyu3zmy1vvevg/pdb.bmp?dl=0 and this is the pdb file dropbox link: https://www.dropbox.com/s/yvxpl2igzi5ccad/120.pdb?dl=0 I used cg algorithm after steep for minimization, too. But it did not work. is there any way to solve this problem? any help is appreciated. On Mon, Oct 5, 2015 at 2:08 PM, Mark Abraham wrote: > 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 < > farideh.kham...@gmail.com> > 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. > -- 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 *
Re: [gmx-users] RDF com
Thanks a lot, Justin. On Sat, Oct 17, 2015 at 8:02 AM, Justin Lemkul wrote: > > > On 10/17/15 5:32 AM, Deva Priya wrote: > >> Hello, >> >> I am trying to calculate the rdf using the center of mass of a sulfonate >> group, SO3 with other SO3 groups in the system. The SO3 group is part of a >> bigger molecule. Is it appropriate to use >> >> gmx rdf -rdf mol_com to carry out this operation or should I use the >> >> > This is correct. > > gmx rdf -yescom >> >> > Boolean options are never prefixed with "yes" so you would have gotten an > obvious fatal error here. > > In each case I would specify the group that contains SO3 atoms twice for >> the rdf calculation. >> >> > Yes. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- 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] RDF com
On 10/17/15 5:32 AM, Deva Priya wrote: Hello, I am trying to calculate the rdf using the center of mass of a sulfonate group, SO3 with other SO3 groups in the system. The SO3 group is part of a bigger molecule. Is it appropriate to use gmx rdf -rdf mol_com to carry out this operation or should I use the This is correct. gmx rdf -yescom Boolean options are never prefixed with "yes" so you would have gotten an obvious fatal error here. In each case I would specify the group that contains SO3 atoms twice for the rdf calculation. Yes. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] radial density profiles gmx
Hello, I am simulating reverse micelles and want to calculate radial density profiles of water trapped inside the RM. I looked up the gmx density, but it looks like it is geared for bilayers. I am wondering if anyone has used gmx density or some other tool to calculate radial density of speciified groups in micellar systems. Any help is greatly appreciated. Thanks, Deva -- 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] RDF com
Hello, I am trying to calculate the rdf using the center of mass of a sulfonate group, SO3 with other SO3 groups in the system. The SO3 group is part of a bigger molecule. Is it appropriate to use gmx rdf -rdf mol_com to carry out this operation or should I use the gmx rdf -yescom In each case I would specify the group that contains SO3 atoms twice for the rdf calculation. Thanks for your help, Deva -- 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.