Re: [gmx-users] mdrun error
Dears all Hi we run a MD simulation. but when we using mdrun command to energy minimization encountered this message: "killed" and No error appears. so anyone can help please? thank you On Mon, Dec 21, 2015 at 10:08 AM, محمد گره گشا <m.gerehgo...@gmail.com> wrote: > Hi all dears > We run a MD simulation. and when we use mdrun command to energy > minimization face this message: 'Killed' and no error. > anyone can help we please? > thanks > -- 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] mdrun error
18 20 dfLIG_ang_53 15 19 21 dfLIG_ang_53 1 22 24 dfLIG_ang_53 2 23 25 dfLIG_ang_53 [ dihedrals ] 3 1 2 6 dfLIG_dih_1 3 1 2 23 dfLIG_dih_1 22 1 2 6 dfLIG_dih_1 22 1 2 23 dfLIG_dih_1 2 1 3 4 dfLIG_dih_1 2 1 3 26 dfLIG_dih_1 22 1 3 4 dfLIG_dih_1 22 1 3 26 dfLIG_dih_1 1 2 6 5 dfLIG_dih_1 1 2 6 27 dfLIG_dih_1 23 2 6 5 dfLIG_dih_1 23 2 6 27 dfLIG_dih_1 1 3 4 5 dfLIG_dih_1 1 3 4 7 dfLIG_dih_1 26 3 4 5 dfLIG_dih_1 26 3 4 7 dfLIG_dih_1 3 4 5 6 dfLIG_dih_1 3 4 5 9 dfLIG_dih_1 7 4 5 6 dfLIG_dih_1 7 4 5 9 dfLIG_dih_1 3 4 7 8 dfLIG_dih_1 3 4 7 28 dfLIG_dih_1 5 4 7 8 dfLIG_dih_1 5 4 7 28 dfLIG_dih_1 4 5 6 2 dfLIG_dih_1 4 5 6 27 dfLIG_dih_1 9 5 6 2 dfLIG_dih_1 9 5 6 27 dfLIG_dih_1 4 5 9 10 dfLIG_dih_1 4 5 9 11 dfLIG_dih_1 6 5 9 10 dfLIG_dih_1 6 5 9 11 dfLIG_dih_1 4 7 8 10 dfLIG_dih_1 4 7 8 29 dfLIG_dih_1 28 7 8 10 dfLIG_dih_1 28 7 8 29 dfLIG_dih_1 7 8 10 9 dfLIG_dih_1 29 8 10 9 dfLIG_dih_1 5 9 10 8 dfLIG_dih_1 11 9 10 8 dfLIG_dih_1 11 12 13 14 dfLIG_dih_1 11 12 13 32 dfLIG_dih_1 16 12 13 14 dfLIG_dih_1 16 12 13 32 dfLIG_dih_1 11 12 16 17 dfLIG_dih_1 11 12 16 33 dfLIG_dih_1 13 12 16 17 dfLIG_dih_1 13 12 16 33 dfLIG_dih_1 12 13 14 15 dfLIG_dih_1 12 13 14 18 dfLIG_dih_1 32 13 14 15 dfLIG_dih_1 32 13 14 18 dfLIG_dih_1 13 14 15 17 dfLIG_dih_1 13 14 15 19 dfLIG_dih_1 18 14 15 17 dfLIG_dih_1 18 14 15 19 dfLIG_dih_1 14 15 17 16 dfLIG_dih_1 14 15 17 34 dfLIG_dih_1 19 15 17 16 dfLIG_dih_1 19 15 17 34 dfLIG_dih_1 12 16 17 15 dfLIG_dih_1 12 16 17 34 dfLIG_dih_1 33 16 17 15 dfLIG_dih_1 33 16 17 34 dfLIG_dih_1 2 1 22 24 dfLIG_dih_1 3 1 22 24 dfLIG_dih_1 1 2 23 25 dfLIG_dih_1 6 2 23 25 dfLIG_dih_1 13 14 18 20 dfLIG_dih_1 15 14 18 20 dfLIG_dih_1 14 15 19 21 dfLIG_dih_1 17 15 19 21 dfLIG_dih_1 5 9 11 12 dfLIG_dih_1 5 9 11 30 dfLIG_dih_1 5 9 11 31 dfLIG_dih_1 10 9 11 30 dfLIG_dih_1 10 9 11 31 dfLIG_dih_1 9 11 12 13 dfLIG_dih_1 9 11 12 16 dfLIG_dih_1 30 11 12 13 dfLIG_dih_1 30 11 12 16 dfLIG_dih_1 31 11 12 13 dfLIG_dih_1 31 11 12 16 dfLIG_dih_1 10 9 11 12 dfLIG_dih_1 14 18 20 35 dfLIG_dih_1 14 18 20 36 dfLIG_dih_1 14 18 20 37 dfLIG_dih_1 15 19 21 38 dfLIG_dih_1 15 19 21 39 dfLIG_dih_1 15 19 21 40 dfLIG_dih_1 1 22 24 41 dfLIG_dih_1 1 22 24 42 dfLIG_dih_1 1 22 24 43 dfLIG_dih_1 2 23 25 44 dfLIG_dih_1 2 23 25 45 dfLIG_dih_1 2 23 25 46 dfLIG_dih_1 Best On Tue, Dec 22, 2015 at 9:06 AM, محمد گره گشا <m.gerehgo...@gmail.com> wrote: > Dears all > Hi > we run a MD simulation. but when we using mdrun command to energy > minimization encountered this message: "killed" and No error appears. > so anyone can help please? > thank you > > On Mon, Dec 21, 2015 at 10:08 AM, محمد گره گشا <m.gerehgo...@gmail.com> > wrote: > >> Hi all dears >> We run a MD simulation. and when we use mdrun command to energy >> minimization face this message: 'Killed' and no error. >> anyone can help we please? >> thanks >> > > -- 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] mdrun error
Hi all dears We run a MD simulation. and when we use mdrun command to energy minimization face this message: 'Killed' and no error. anyone can help we please? thanks -- 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] grompp error
All Deadr Hi we want to run a protein-ligand MD simulation, when we use mdrun (mdrun -s em.tpr -nt 4 -o em.trr -c complexpr.gro -e em.edr) we have not any error but the run written killed: Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps = 400 Killed can anyone help please? thanks On Sun, Oct 18, 2015 at 10:36 AM, محمد گره گشا <m.gerehgo...@gmail.com> wrote: > All dears > > > we doing MD by oplsa ff for protein-ligand complex that we take from > Autodock. we do this steps to add ligand as a residue at residue database, > but when run grompp we face this error > > ERROR 1 [ file LIG.itp, line 401 ]: > >No default proper Dih. types > > Fatal error: > > There was 1 error in input file(s) > > > > can you help we please? > > so thank you. > > We attached LIG.itp > -- 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] grompp error
All dears we doing MD by oplsa ff for protein-ligand complex that we take from Autodock. we do this steps to add ligand as a residue at residue database, but when run grompp we face this error ERROR 1 [ file LIG.itp, line 401 ]: No default proper Dih. types Fatal error: There was 1 error in input file(s) can you help we please? so thank you. We attached LIG.itp -- 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] grompp error
All dears we doing MD by oplsa ff for protein-ligand complex that we take from Autodock. we do this steps to add ligand as a residue at residue database, but when run grompp we face this error ERROR 1 [ file LIG.itp, line 401 ]: No default proper Dih. types Fatal error: There was 1 error in input file(s) can you help we please? so thank you. We attached LIG.itp -- 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] grompp error
All dears we run MD for protein-ligand complex that we take from Autodock. but when we run grompp we face this error: ERROR 1 [ file LIG.itp, line 401 ] No default Proper Dih. types Fatal error: There was 1 error in input file(s) can any 1 help we to resolve this error pleas? we attached LIG.itp -- 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.org_gmx-users Digest, Vol 134, Issue 45
Hi everyone I'm going to run md simulation but when i use grompp command i face this warning: WARNING 1 [file DRGGMX.ITP, line 18]: Too few parameters on line (source file toppush.c, line 731) can everyone help me please? On Mon, Jun 8, 2015 at 2:18 PM, gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than Re: Contents of gromacs.org_gmx-users digest... Today's Topics: 1. Re: Problems installing gromacs 5.0.4 with plumed 2.1.2 for MPI (jkrie...@mrc-lmb.cam.ac.uk) 2. Re: Microwave (Mostafa Javaheri) 3. gmx distance (Poncho Arvayo Zatarain) 4. cudaStreamSynchronize failed in cu_blockwait_nb (Alex) 5. Re: cudaStreamSynchronize failed in cu_blockwait_nb (Alex) 6. Immediate PhD Opening In Computational Structural Biology Of Membrane Proteins (Marawan Hussien) -- Message: 1 Date: Mon, 8 Jun 2015 18:57:37 +0100 From: jkrie...@mrc-lmb.cam.ac.uk To: James Krieger jkrie...@mrc-lmb.cam.ac.uk Cc: gmx users-list gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Problems installing gromacs 5.0.4 with plumed 2.1.2 for MPI Message-ID: f747d8a83bda90990801c5edbe619a2c.squir...@mail.mrc-lmb.cam.ac.uk Content-Type: text/plain More details are available on the plumed forum google group at https://groups.google.com/forum/?utm_medium=emailutm_source=footer#!msg/plumed-users/stlK9-kaa6A/jSm8rOON_xsJ Hi, I have successfully installed plumed-2.1.2 (I believe with MPI capabilities) and patched it onto gromacs-5.0.4, I am now trying to install the gromacs and it's not working. Here are my errors from make: collect2: error: ld returned 1 exit status src/gromacs/CMakeFiles/libgromacs.dir/build.make:22956: recipe for target 'lib/libgromacs_mpi.so.0.0.0' failed make[2]: *** [lib/libgromacs_mpi.so.0.0.0] Error 1 CMakeFiles/Makefile2:1948: recipe for target 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2 Makefile:146: recipe for target 'all' failed make: *** [all] Error 2 I have successfully installed the latest gcc compilers and tried to tell gromacs to use them with the following command (not sure if this is right): ccmake ../gromacs-5.0.4/ -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_C_COMPILER=/lmb/home/jkrieger/bin/gcc-5.1.0-build/bin/gcc In any case I get similar errors using the default compilers on my system. I am installing on a front-end node of our cluster at the LMB, which has a shared filesystem. Please let me know if there's anything else I need to tell you so that you can help. Many thanks James -- Message: 2 Date: Mon, 8 Jun 2015 22:34:02 +0430 From: Mostafa Javaheri javaheri.grom...@gmail.com To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Microwave Message-ID: CAH0JJJKJdmfYA=Yvt= jdsenaiuwdtweexrau0lz2dndjtkr...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Dear Mark, The authors didn't circulate the modified version of GROMACS and they couldn't be able for any help. It would be very kind of you if you could give me some information about which file or files of the source code should I alter for achieving this purpose. Best, Mostafa On Mon, Jun 8, 2015 at 8:05 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, You'd have to contact the authors to get their modified version. Mark On Sun, Jun 7, 2015 at 11:09 PM Mostafa Javaheri javaheri.grom...@gmail.com wrote: Hi all, Thanks for your replies, I searched about the simulation under e/m field and as far as I understood, I have to alter the source code for that, but I don't know how to do this and which part of the source code must change exactly. several studies have been performed by Niall J. English and co ( http://scitation.aip.org/content/aip/journal/jcp/131/3/10.1063/1.3184794 ) and (http://adsabs.harvard.edu/abs/2003JChPh.118.1589E) which I'm tending to do the same but with different protein, due to the correspondence, they used modified version of GROMACS 3 in their studies. I would be thankful if you could give me some idea about this kind of modification? Best, Mostafa On Tue, Jun 2, 2015 at 4:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/2/15
[gmx-users] Hi
I am going to run md but when i use grompp command i face this warning: WARNING 1 [file DRGGMX.ITP, line 18]: Too few parameters on line (source file toppush.c, line 731) can everyone help me please? -- 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.
