[gmx-users] Incorrect number of parameters - found 3, expected 1 or 1 for Polarization.
Dear all, I used Gromacs 5.0.5 to generate a trajectory of polarizable water system with SWM4-NDP model, and then tried to use a custom version Gromacs 4.5.5 to calculate local pressure of the system. When I generate the .tpr file with Gromacs 4.5.5, an error coccurs: Fatal error: Incorrect number of parameters - found 3, expected 1 or 1 for Polarization. What does this mean? How should I solve this problem? Any help will be appreciated! Best wishes, Xiaohui She University of Wisconsin-Madison -- 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] Incorrect number of parameters - found 3, expected 1 or 1 for Polarization.
On 8/20/15 1:03 PM, 折晓会 wrote: Dear all, I used Gromacs 5.0.5 to generate a trajectory of polarizable water system with SWM4-NDP model, and then tried to use a custom version Gromacs 4.5.5 to calculate local pressure of the system. When I generate the .tpr file with Gromacs 4.5.5, an error coccurs: Fatal error: Incorrect number of parameters - found 3, expected 1 or 1 for Polarization. What does this mean? How should I solve this problem? This means that you have too many parameters on some line related to the [polarization] directive. Isotropic polarization takes one value (alpha), so that's all that is allowed. -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] High load imbalance: 31.8%
Hi Anthony, Good choice, your admins should be able to help. Do emphasize when talking to them that you need your job to be placed as compact as possible, on the closest possible set of cores with the tightest possible affinity settings. Cheers, -- Szilárd On Thu, Aug 20, 2015 at 6:12 PM, Nash, Anthony a.n...@ucl.ac.uk wrote: Hi Szilárd Thanks for all of that advice. I’m going to have to take a lot of this up with the Cluster Service Staff. This is a new cluster service I won a grant for, thus not my usual platform which would typically yield an imbalance of somewhere around 0.8% to 2%. Thanks again Anthony On 20/08/2015 16:52, Szilárd Páll pall.szil...@gmail.com wrote: Hi, You're not pinning threads and it seems that you're running on a large SMP machine! Assuming that the 512 threads reported (line 91) is correct that's a 32 socket SMP machine, perhaps an SGI UV? In any case Xeon E5-4xxx is typically deployed in 4-8 socket installations, so your 8 threads will be floating around on a number of CPUs which ruins your performance - and likely contributes to the varying and large load imbalance. My advice: - don't ignore notes/warnings issued by mdrun (line 366, should be on the standard out too), we put quite some though into spamming users only when relevant :) - pin mdrun and/or its threads either with -pin on (and -pinoffset if needed) or with whatever tools your admins provide/recommend [Extras: consider using FFTW even with the Intel compilers it's often faster for our small FFTs than MKL; and GNU iso Intel compiler is often faster too.] Fixing the above issues should not only reduce imbalance but most likely also allow you to gain quite some simulation performance! Let us know if it worked. Cheers, -- Szilárd On Thu, Aug 20, 2015 at 5:08 PM, Nash, Anthony a.n...@ucl.ac.uk wrote: Hi Mark, Many thanks for looking into this. One of the log files (the job hasn’t finished running) is here: https://www.dropbox.com/s/zwrro54yni2uxtn/umb_3_umb.log?dl=0 The system is a soluble collagenase in water with a collagen substrate and two zinc co-factors. There are 287562 atoms in the system. Please let me know if you need to know anything else. Thanks! Anthony On 20/08/2015 11:39, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, In cases like this, it's good to describe what's in your simulation, and share the full .log file on a file-sharing service, so we can see both the things mdrun reports early and late. Mark On Thu, Aug 20, 2015 at 8:22 AM Nash, Anthony a.n...@ucl.ac.uk wrote: Hi all, I appear to have a very high load imbalance on some of my runs. Values starting from approx. 7% up to 31.8% with reported vol min/aver of around 0.6 (I haven¹t found one under half yet). When I look through the .log file at the start of the run I see: Initializing Domain Decomposition on 8 ranks Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 0.514 nm, LJ-14, atoms 3116 3123 multi-body bonded interactions: 0.429 nm, Proper Dih., atoms 3116 3123 Minimum cell size due to bonded interactions: 0.472 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.862 nm Estimated maximum distance required for P-LINCS: 0.862 nm This distance will limit the DD cell size, you can override this with -rcon Using 0 separate PME ranks, as there are too few total ranks for efficient splitting Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 8 cells with a minimum initial size of 1.077 nm The maximum allowed number of cells is: X 12 Y 12 Z 12 Domain decomposition grid 4 x 2 x 1, separate PME ranks 0 PME domain decomposition: 4 x 2 x 1 Domain decomposition rank 0, coordinates 0 0 0 Using 8 MPI processes Using 1 OpenMP thread per MPI process Having a quick look through the documentation and I see that I should consider implementing the verlet cut-off (which I am) and adjust the number of PME nodes/cut-off and PME grid spacing. Would this simply be a case of throwing more cores at the simulation or must I play around with P-LINCS parameters? Thanks Anthony -- 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
[gmx-users] High load imbalance: 31.8%
Hi all, I appear to have a very high load imbalance on some of my runs. Values starting from approx. 7% up to 31.8% with reported vol min/aver of around 0.6 (I haven¹t found one under half yet). When I look through the .log file at the start of the run I see: Initializing Domain Decomposition on 8 ranks Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 0.514 nm, LJ-14, atoms 3116 3123 multi-body bonded interactions: 0.429 nm, Proper Dih., atoms 3116 3123 Minimum cell size due to bonded interactions: 0.472 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.862 nm Estimated maximum distance required for P-LINCS: 0.862 nm This distance will limit the DD cell size, you can override this with -rcon Using 0 separate PME ranks, as there are too few total ranks for efficient splitting Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 8 cells with a minimum initial size of 1.077 nm The maximum allowed number of cells is: X 12 Y 12 Z 12 Domain decomposition grid 4 x 2 x 1, separate PME ranks 0 PME domain decomposition: 4 x 2 x 1 Domain decomposition rank 0, coordinates 0 0 0 Using 8 MPI processes Using 1 OpenMP thread per MPI process Having a quick look through the documentation and I see that I should consider implementing the verlet cut-off (which I am) and adjust the number of PME nodes/cut-off and PME grid spacing. Would this simply be a case of throwing more cores at the simulation or must I play around with P-LINCS parameters? Thanks Anthony -- 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] atom types IP and IM
Hi; I've used ff14sbamber force field to generate my system. As this force field doesn'texist in gromacs, I generated the first structure of my system withamber tools then I converted the topology and coordinate files intogromacs format by using acpype. (In the amber tools I've added NaClto my system). Now in the converted topology file I have these lines: [ moleculetype ] ; molname nrexcl NA+ 1 [ atoms ] ; id_ at typeres nr residu name at name cg nr charge mass 1 IP 1 NA+ NA+ 1 1 22.9898 [ moleculetype ] ; molname nrexcl CL- 1 [ atoms ] ; id_ at typeres nr residu name at name cg nr charge mass 1 IM 1 CL- CL- 1 -1 35.45300 As we can see, wehave IP and IM atom types for Na+ and Cl- ions respectively. When Iwant to run energy minimization with the grompp command I get thiserror: Fatal error: Atomtype IP not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I think that itcannot recognize IP atom type. What should I do? 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] Incorrect number of parameters - found 3, expected 1 or 1 for Polarization.
On 8/20/15 6:05 PM, 折晓会 wrote: Thank you professor Justin! I solved this error which comes from the decimals of the box dimensions. Initially, my box dimensions are 4.5*4.5*16 nm3 and the local pressure calculation does not work, but after I change them to be integers 4*4*16 nm3 in the gro file, the simulation works. It is strange for me. I do not know why. I fail to see how making the box smaller solves a box too small error, and moreover, making changes like this is going to affect the results. Don't consider this a solution. Probably an indication of a bug. So you're just reading in a .gro file? Does a single coordinate file trigger the error before, or was that from an actual trajectory? -Justin Best wishes, Xiaohui Date: Thu, 20 Aug 2015 16:44:58 -0400 From: jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Incorrect number of parameters - found 3, expected 1 or 1 for Polarization. On 8/20/15 4:01 PM, 折晓会 wrote: Thank you professor Justin! I solved this error with your suggestion. When I use mdrun -rerun to calculate the local pressure, another error occurs: Fatal error: Rerun trajectory frame step 60 time 600.00 has too small box dimensions What does this mean? It means your box is too small. What are the box dimensions in that frame, and what are the cutoffs you are using? -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. -- == 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] AIX XLC Gromacs-5.1-rc1. Undefined reference. Underscore issue.
Hi, GROMACS 5.1 is out, please don't install 5.1-rc1 any more. There's a little bit of advice about using custom linear algebra libraries at http://manual.gromacs.org/documentation/5.1/install-guide/index.html#linear-algebra-libraries but you don't need to bother with such libraries unless you know mdrun will be used to do normal-mode analysis or something. You might still run into problems - if so, we'll want to know how you ran cmake in the first place. Mark On Thu, Aug 20, 2015 at 1:20 AM Carlos Aguni sorla...@gmail.com wrote: Helo guys! I'm trying to compile Gromacs-5.1-rc1 with XLC 13.1.2 ESSL 5.3 and I'm facing an undefined reference error. Here's what I got: $ cd /home/ibm/crash/gromacs-agosto/2/gromacs-5.1-rc1/single/share/template /usr/bin/cmake -E cmake_link_script CMakeFiles/template.dir/link.txt --verbose=1 $ /usr/bin/mpixlc++-qarch=auto -qaltivec -std=c++0x -qnoinline -O0 -qsmp=omp -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -O3 -DNDEBUG -qextname CMakeFiles/template.dir/template.cpp.o -o ../../bin/template -rdynamic ../../lib/libgromacs_mpi.so.1.0.0 -ldl -lrt -lessl -L/usr/lib -lessl -L/opt/ibm/xlf/15.1.2/lib/ -lxlf90 -lxlf90_t -Wl,-rpath,\$ORIGIN/../lib /opt/ibm/xlC/13.1.2/bin/.orig/xlc++: warning: 1501-218 file ../../lib/libgromacs_mpi.so.1.0.0 contains an incorrect file suffix ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `dlaev2_' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `dorm2r_' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `gmx_fft_init_1d_real' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `dlascl_' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `slaev2_' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `slarnv_' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `slartg_' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `dlasr_' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `gmx_fft_init_2d_real' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `ssyevr_' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `gmx_fft_1d_real' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `slasr_' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `sorm2r_' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `dlaset_' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `slacpy_' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `dlapy2_' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `dlarnv_' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `gmx_fft_get_version_info' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `gmx_fft_1d' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `slanst_' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `dgeqr2_' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `sgeqr2_' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `gmx_fft_cleanup' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `ssteqr_' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `dsteqr_' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `dlacpy_' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `slapy2_' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `dlartg_' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `gmx_fft_destroy' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `slascl_' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `slaset_' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `dlanst_' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `gmx_fft_2d_real' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `gmx_fft_init_1d' I think that's an underscore problem. Because ESSL has those functions but the flags responsible to solve that (-qextname -qnoextname) isn't working: $ objdump -x /usr/lib/libessl.so | grep dlaev2 ldf *ABS* /home/essl/src/work/dlaev2.f 00aa67a0 l F .text 023c 0x60 dlaev2 $ objdump -x /usr/lib/libessl.so | grep dlacpy ldf *ABS* /home/essl/src/work/dlacpyd.f ldf *ABS* /home/essl/src/work/dlacpy.f 00a99ca0 l F .text 0440 0x60 dlacpyd 00a9a0e0 l F .text 03b0 0x60 dlacpy Can anyone help? Thanks in advance! Carlos. -- 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] Adding HSD residue to AMBER ff99SB-ILDN
On 8/20/15 3:17 AM, Simone Bolognini wrote: Hi everyone, I have a .pdb file of the WW domain of human FIP35 protein extracted from an MD calculation obtained with AMBER ff99SB-ILDN and solvent type tip3. Now I need to obtain the topology out of it, but the .pdb contains a residue, namely HSD, which is not present in the Amber residue database. I looked at the source files and found out that CHARMM has it. In particular, this is what you can find in the CHARMM database: [ HSD ] [ atoms ] N NH1 -0.47 0 HN H 0.31 1 CA CT1 0.07 2 HA HB 0.09 3 CB CT2 -0.09 4 HB1 HA 0.09 5 HB2 HA 0.09 6 ND1 NR1 -0.36 7 HD1 H 0.32 8 CG CPH1 -0.05 9 CE1 CPH2 0.25 10 HE1 HR1 0.13 11 NE2 NR2 -0.70 12 CD2 CPH1 0.22 13 HD2 HR3 0.10 14 C C 0.51 15 O O -0.51 16 [ bonds ] CB CA CG CB ND1 CG CE1 ND1 NE2 CD2 N HN N CA C CA C +N CA HA CB HB1 CB HB2 ND1 HD1 CD2 HD2 CE1 HE1 O C CG CD2 CE1 NE2 [ impropers ] ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 ND1 CE1 CG HD1 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 N -C CA HN C CA +N O [ cmap ] -C N CA C +N Is there any possible way in which I can copy and paste this in the Amber database and hope it will work correctly? Thank you very much!!! No, you can't copy and paste, because then you're mixing force fields and that is bad practice. HSD is just delta-protonated HIS, which is already in AMBER. It's just called HID, so rename your coordinate files appropriately and you can generate the topology. -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] CHARMM forcefield parameters for carbon naotubes
On 8/20/15 7:53 AM, Sanchaita Rajkhowa wrote: Dear all, I am trying to simulate a carbon nano-tube using CHARMM27 forcefield but I can't get it right. I have been following the modeling carbon nano-tubes with gromacs (http://chembytes.wikidot.com/grocnt) but it is done using opls-aa forcefield. I have tried in a similar way and I keep getting errors: --- Opening force field file ./test.ff/ffcharmm.n2t There are 5 name to type translations in file ./test.ff Generating bonds from distances... atom 80 There are 1 different atom types in your sample Generating angles and dihedrals from bonds... Segmentation fault (core dumped) --- If anyone has done the simulation of a CNT using CHARMM27 forcefield then please help. Make sure use version 5.1 as a bug that caused this seg fault was fixed. Anything in the 5.0.x series will be affected (and IIRC also 4.6.6). -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] Adding HSD residue to AMBER ff99SB-ILDN
Thank you for your answer! I did it and now gromacs throws me the following error: Atom HG1 in residue SER 2 was not found in rtp entry SER with 11 atoms while sorting atoms.. Any clue? Thank you very much. Il giorno gio 20 ago 2015 alle ore 13:18 Justin Lemkul jalem...@vt.edu ha scritto: On 8/20/15 3:17 AM, Simone Bolognini wrote: Hi everyone, I have a .pdb file of the WW domain of human FIP35 protein extracted from an MD calculation obtained with AMBER ff99SB-ILDN and solvent type tip3. Now I need to obtain the topology out of it, but the .pdb contains a residue, namely HSD, which is not present in the Amber residue database. I looked at the source files and found out that CHARMM has it. In particular, this is what you can find in the CHARMM database: [ HSD ] [ atoms ] N NH1 -0.47 0 HN H 0.31 1 CA CT1 0.07 2 HA HB 0.09 3 CB CT2 -0.09 4 HB1 HA 0.09 5 HB2 HA 0.09 6 ND1 NR1 -0.36 7 HD1 H 0.32 8 CG CPH1 -0.05 9 CE1 CPH2 0.25 10 HE1 HR1 0.13 11 NE2 NR2 -0.70 12 CD2 CPH1 0.22 13 HD2 HR3 0.10 14 C C 0.51 15 O O -0.51 16 [ bonds ] CB CA CG CB ND1 CG CE1 ND1 NE2 CD2 N HN N CA C CA C +N CA HA CB HB1 CB HB2 ND1 HD1 CD2 HD2 CE1 HE1 O C CG CD2 CE1 NE2 [ impropers ] ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 ND1 CE1 CG HD1 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 N -C CA HN C CA +N O [ cmap ] -C N CA C +N Is there any possible way in which I can copy and paste this in the Amber database and hope it will work correctly? Thank you very much!!! No, you can't copy and paste, because then you're mixing force fields and that is bad practice. HSD is just delta-protonated HIS, which is already in AMBER. It's just called HID, so rename your coordinate files appropriately and you can generate the topology. -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] High load imbalance: 31.8%
Hi, In cases like this, it's good to describe what's in your simulation, and share the full .log file on a file-sharing service, so we can see both the things mdrun reports early and late. Mark On Thu, Aug 20, 2015 at 8:22 AM Nash, Anthony a.n...@ucl.ac.uk wrote: Hi all, I appear to have a very high load imbalance on some of my runs. Values starting from approx. 7% up to 31.8% with reported vol min/aver of around 0.6 (I haven¹t found one under half yet). When I look through the .log file at the start of the run I see: Initializing Domain Decomposition on 8 ranks Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 0.514 nm, LJ-14, atoms 3116 3123 multi-body bonded interactions: 0.429 nm, Proper Dih., atoms 3116 3123 Minimum cell size due to bonded interactions: 0.472 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.862 nm Estimated maximum distance required for P-LINCS: 0.862 nm This distance will limit the DD cell size, you can override this with -rcon Using 0 separate PME ranks, as there are too few total ranks for efficient splitting Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 8 cells with a minimum initial size of 1.077 nm The maximum allowed number of cells is: X 12 Y 12 Z 12 Domain decomposition grid 4 x 2 x 1, separate PME ranks 0 PME domain decomposition: 4 x 2 x 1 Domain decomposition rank 0, coordinates 0 0 0 Using 8 MPI processes Using 1 OpenMP thread per MPI process Having a quick look through the documentation and I see that I should consider implementing the verlet cut-off (which I am) and adjust the number of PME nodes/cut-off and PME grid spacing. Would this simply be a case of throwing more cores at the simulation or must I play around with P-LINCS parameters? Thanks Anthony -- 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] trjconv -dt issue
Hi, This is indeed problematic. The .edr format (and its tools) are designed with limitations that were not really a problem 10 years ago. One of the limitations is that the time itself is stored in the same precision as the simulation data, and this starts to lose precision as the simulation proceeds into the millions of MD steps. I think your practical course is to keep the simulation in the chunks that you already have, and do your subsampling from them. You may get a better result if you pre-process each chunk to start from zero time (or making smaller chunks if you need to). This will help by keeping the side of the stride closer to the absolute value of the time. Another alternative is to pre-process the chunks with a double-precision eneconv, which will write the times in double precision. That won't help if they're stored wrongly in the first place, but may help you handle some longer trajectory (at cost of more disk space). Mark On Wed, Aug 19, 2015 at 11:50 PM Matthias Ernst matthias.er...@physik.uni-freiburg.de wrote: Hello, I have a quite long continuous trajectory coming from several initial input pieces (cluster crashed...) that I want to downsample, as a start from 0.5ps timestep in the source files to just 1ps and later bigger timesteps. Using the -dt option of trjconv (GROMACS 4.6.5.), there seem to be rounding issues which leads to times at .5ps being written from some timestamp on (4.1943e+06). Is this a known behaviour? Related to this, what does the following sentence in the help for trjconv -dt mean: This option relies on the accuracy of the times in your input trajectory, so if these are inaccurate use the -timestep option to modify the time (this can be done simultaneously). How can I change the input timestep to get a proper output of output frames? I tried to use -timestep 1 it to my trajectory with 0.5ps timestep and it seems to produce correct timestamps in 1ps steps in the output file but the coordinates still are those of the initial frames with the 0.5ps timestamps, meaning it just relabels the timestamps of the frames. Using -timestep 0.5 -dt 1 together does not change the result compared to -dt 1 only. If I rather use the -t0 0 option, I can reset the time of the first frame and then, it looks like it writes the correct 1ps stepped frames with 1ps timestamps, but starting at time 0. As I have several trajectory pieces from a continuous timeseries to concatenate, I would have to run trjconv once more just to correct and reset the time to its initial value, which means a lot of unnecessary data transfer, especially in the case of long trajectories. Is this really necessary or is there another way to get a proper downsampling? I know I can use the -skip 2 option but e.g. not for eneconv which only supports -dt and has the same issues. Further, just using -skip 2 is not possible if some input files are at 0.5ps, but some other already at 1ps time steps. Thank you for your help, Matthias -- Progress... http://www.phdcomics.com/comics/archive.php?comicid=1611 -- 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] CHARMM forcefield parameters for carbon naotubes
Dear all, I am trying to simulate a carbon nano-tube using CHARMM27 forcefield but I can't get it right. I have been following the modeling carbon nano-tubes with gromacs (http://chembytes.wikidot.com/grocnt) but it is done using opls-aa forcefield. I have tried in a similar way and I keep getting errors: --- Opening force field file ./test.ff/ffcharmm.n2t There are 5 name to type translations in file ./test.ff Generating bonds from distances... atom 80 There are 1 different atom types in your sample Generating angles and dihedrals from bonds... Segmentation fault (core dumped) --- If anyone has done the simulation of a CNT using CHARMM27 forcefield then please help. Thank you. Regards, Sanchaita. -- 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] Adding HSD residue to AMBER ff99SB-ILDN
Well... that was a rookie mistake. Sorry about that. Thank you! Il giorno gio 20 ago 2015 alle ore 14:18 Justin Lemkul jalem...@vt.edu ha scritto: On 8/20/15 8:16 AM, Simone Bolognini wrote: Thank you for your answer! I did it and now gromacs throws me the following error: Atom HG1 in residue SER 2 was not found in rtp entry SER with 11 atoms while sorting atoms.. Any clue? Thank you very much. pdb2gmx -ignh -Justin Il giorno gio 20 ago 2015 alle ore 13:18 Justin Lemkul jalem...@vt.edu ha scritto: On 8/20/15 3:17 AM, Simone Bolognini wrote: Hi everyone, I have a .pdb file of the WW domain of human FIP35 protein extracted from an MD calculation obtained with AMBER ff99SB-ILDN and solvent type tip3. Now I need to obtain the topology out of it, but the .pdb contains a residue, namely HSD, which is not present in the Amber residue database. I looked at the source files and found out that CHARMM has it. In particular, this is what you can find in the CHARMM database: [ HSD ] [ atoms ] N NH1 -0.47 0 HN H 0.31 1 CA CT1 0.07 2 HA HB 0.09 3 CB CT2 -0.09 4 HB1 HA 0.09 5 HB2 HA 0.09 6 ND1 NR1 -0.36 7 HD1 H 0.32 8 CG CPH1 -0.05 9 CE1 CPH2 0.25 10 HE1 HR1 0.13 11 NE2 NR2 -0.70 12 CD2 CPH1 0.22 13 HD2 HR3 0.10 14 C C 0.51 15 O O -0.51 16 [ bonds ] CB CA CG CB ND1 CG CE1 ND1 NE2 CD2 N HN N CA C CA C +N CA HA CB HB1 CB HB2 ND1 HD1 CD2 HD2 CE1 HE1 O C CG CD2 CE1 NE2 [ impropers ] ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 ND1 CE1 CG HD1 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 N -C CA HN C CA +N O [ cmap ] -C N CA C +N Is there any possible way in which I can copy and paste this in the Amber database and hope it will work correctly? Thank you very much!!! No, you can't copy and paste, because then you're mixing force fields and that is bad practice. HSD is just delta-protonated HIS, which is already in AMBER. It's just called HID, so rename your coordinate files appropriately and you can generate the topology. -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. -- == 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] Error while configuring gmx-3.3.1
Hi, Apparently the 3.3.1 install isn't working well for you. You can use cp -R gromacs-3.3.1/share/top/* /usr/local/gromacs/share/top/ which is a standard unix command. Mark On Thu, Aug 20, 2015 at 5:52 AM Padmani Sandhu padmanisandh...@gmail.com wrote: Hello Justin, I have copied both the .itp files which were giving error in to /usr/local/gromacs/share/top using command: sudo cp BH4_oplsaa.itp /usr/local/gromacs/share/top sudo cp ffoplsaabon.itp /usr/local/gromacs/share/top and now grompp worked. Please can you suggest me any solution so that all the files in *gromacs-3.3.1/share/top *can be copied to */usr/local/gromacs/share/top.* Thanks Padmani On Wed, Aug 19, 2015 at 5:42 PM, Padmani Sandhu padmanisandh...@gmail.com wrote: 1. I am using it with CPMD as they have mentioned this version of gromacs only. 2. The top-level force fields are not included as they are not present in /usr/local/gromacs/share/top/ file for eg. BH4_oplsaa.itp, however its there in the gmx-3.3.1_qmmm-1.3.2/share/top folder. 3. There is no problem with topology, its working fine with gromacs-4.5.6 and later versions. Thanks Padmani On Wed, Aug 19, 2015 at 5:32 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/19/15 7:58 AM, Padmani Sandhu wrote: Hello everyone, I am trying to install gmx-3.3.1 on ubuntu 14.04. I have compiled it using following commands: Any reason you're using wildly outdated software? ./configure make sudo make install *However the program was installed but while running grommp, it was terminated with an error :* checking input for internal consistency... calling cpp... In file included from /usr/local/gromacs/share/top/ffoplsaa.itp:23:0, from topol.top:11: /usr/local/gromacs/share/top/ffoplsaabon.itp:2692:26: fatal error: BH4_oplsaa.itp: No such file or directory #include BH4_oplsaa.itp ^ compilation terminated. You probably shouldn't be #including files in top-level force field files. cpp exit code: 256 Tried to execute: 'cpp -I/usr/local/gromacs/share/top topol.top gromppVUW784' The 'cpp' command is defined in the .mdp file processing topology... processing coordinates... --- Program grompp, VERSION 3.3.1 Source code file: grompp.c, line: 448 Fatal error: number of coordinates in coordinate file (conf_solv.gro, 317253) does not match topology (topol.top, 0) Your topology is totally wrong or misformatted. *I had an error while running ./configure that might be causing this problem* configure: creating ./config.status config.status: creating Makefile config.status: WARNING: Makefile.in seems to ignore the --datarootdir setting config.status: creating src/Makefile config.status: WARNING: src/Makefile.in seems to ignore the --datarootdir setting This is not related. -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. -- *Padmani sandhu* *Research Scholar,* *Center for Computational Biology and Bioinformatics,* *Central University of Himachal Pradesh,* *Temporary Academic Block, Shahpur * *Pin 176206, District Kangra,* *Himachal Pradesh, India* -- *Padmani sandhu* *Research Scholar,* *Center for Computational Biology and Bioinformatics,* *Central University of Himachal Pradesh,* *Temporary Academic Block, Shahpur * *Pin 176206, District Kangra,* *Himachal Pradesh, India* -- 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
[gmx-users] A query about nsteps
Dear gromcas users, I carried out a continuation of previous md run for nsteps of 500 and dt of 0.002 using the following commands, gmx grompp -f md.mdp -o md2.tpr -c md1.gro -t md1.cpt -r ref.pdb -n index.ndx -p topol.top gmx_mpi mdrun -cpi md1.cpt -deffnm md2 The mdp file following run parameters, *** integrator = md dt = 0.002 nsteps = 500 ; nstlog = 1000 nstxout = 0 nstvout = 0 nstfout = 0 nstcalcenergy = 100 nstenergy = 1000 nstxout-compressed = 2 compressed-x-grps = System ; cutoff-scheme = Verlet nstlist = 20 rlist = 1.2 coulombtype = pme rcoulomb= 1.2 vdwtype = Cut-off vdw-modifier= Force-switch rvdw_switch = 1.0 rvdw= 1.2 ; pbc = xyz ; gen_vel = no ; tcoupl = Nose-Hoover tc_grps = Protein POPC CL_SOL tau_t = 0.50.5 0.5 ref_t = 305.0305.0305.0 ; pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 5.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 ; constraints = h-bonds constraint_algorithm= LINCS continuation= yes ; nstcomm = 100 comm_mode = linear comm_grps = Protein_POPC CL_SOL ; refcoord_scaling= com ** Though the run completed successfully, I just noticed from the log file that the simulation carried out only for 350 steps, instead of 500 steps. It looks to me that the simulation started from the previous run that completed 150 steps and the current run went from the next 350 steps to complete the total run for 500 steps. Why this happened? Why it counted total run as 500 steps rather than continue the current for another 500 steps? Also, I also noticed that the XTC file is written with 176 frames instead of 175 frames (i.e. 350/2)? Is it writing the last step of the previous run again? Below is the head and tail of the log file. *** Started mdrun on rank 0 Wed Aug 19 13:21:50 2015 Step Time Lambda 150 3000.00.0 Energies (kJ/mol) BondU-BProper Dih. Improper Dih. CMAP Dih. 2.68385e+041.29842e+059.81752e+042.12606e+031.22039e+02 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. 1.92413e+04 -3.79314e+048.94538e+04 -2.15678e+068.56903e+03 Position Rest. PotentialKinetic En. Total Energy 1.19967e+03 -1.81913e+064.40840e+05 -1.37829e+06 Temperature Pressure (bar) Constr. rmsd 3.05915e+029.88325e+013.99434e-06 DD step 1500024 load imb.: force 23.7% pme mesh/force 0.689 At step 1500025 the performance loss due to force load imbalance is 10.2 % NOTE: Turning on dynamic load balancing DD load balancing is limited by minimum cell size in dimension Z DD step 1500999 vol min/aver 0.797! load imb.: force 2.1% pme mesh/force 1.021 Step Time Lambda 1501000 3002.00.0 Energies (kJ/mol) BondU-BProper Dih. Improper Dih. CMAP Dih. 2.69950e+041.30117e+059.81626e+042.14421e+033.04253e+02 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. 1.92568e+04 -3.91777e+048.75313e+04 -2.15233e+068.72461e+03 Position Rest. PotentialKinetic En. Total Energy 1.12669e+03 -1.81713e+064.39962e+05 -1.37717e+06 Temperature Pressure (bar) Constr. rmsd 3.05306e+02 -1.47275e+023.98818e-06 - - - Step Time Lambda 5001.00.0 Writing checkpoint, step 500 at Wed Aug 19 22:49:38 2015 Energies (kJ/mol) BondU-BProper Dih. Improper Dih. CMAP Dih. 2.71898e+041.29717e+059.78396e+042.14084e+031.91548e+02 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. 1.92444e+04 -3.67507e+049.10908e+04 -2.16220e+068.48970e+03 Position Rest. PotentialKinetic En. Total Energy 1.2e+03 -1.82178e+064.38586e+05 -1.38319e+06 Temperature Pressure (bar) Constr. rmsd 3.04350e+027.56441e+013.99781e-06 == ### ==
Re: [gmx-users] A query about nsteps
On 8/20/15 7:49 AM, anu chandra wrote: Dear gromcas users, I carried out a continuation of previous md run for nsteps of 500 and dt of 0.002 using the following commands, gmx grompp -f md.mdp -o md2.tpr -c md1.gro -t md1.cpt -r ref.pdb -n index.ndx -p topol.top gmx_mpi mdrun -cpi md1.cpt -deffnm md2 This is redundant. If you restart like this (you should use gmx convert-tpr for simple extensions, as grompp has issues preserving pressure coupling information), then you don't need -cpi when executing mdrun. The mdp file following run parameters, *** integrator = md dt = 0.002 nsteps = 500 ; nstlog = 1000 nstxout = 0 nstvout = 0 nstfout = 0 nstcalcenergy = 100 nstenergy = 1000 nstxout-compressed = 2 compressed-x-grps = System ; cutoff-scheme = Verlet nstlist = 20 rlist = 1.2 coulombtype = pme rcoulomb= 1.2 vdwtype = Cut-off vdw-modifier= Force-switch rvdw_switch = 1.0 rvdw= 1.2 ; pbc = xyz ; gen_vel = no ; tcoupl = Nose-Hoover tc_grps = Protein POPC CL_SOL tau_t = 0.50.5 0.5 ref_t = 305.0305.0305.0 ; pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 5.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 ; constraints = h-bonds constraint_algorithm= LINCS continuation= yes ; nstcomm = 100 comm_mode = linear comm_grps = Protein_POPC CL_SOL ; refcoord_scaling= com ** Though the run completed successfully, I just noticed from the log file that the simulation carried out only for 350 steps, instead of 500 steps. It looks to me that the simulation started from the previous run that completed 150 steps and the current run went from the next 350 steps to complete the total run for 500 steps. Why this happened? Why it counted total run as 500 steps rather than continue the current for another 500 steps? Yes, because of the redundancy above. Also, I also noticed that the XTC file is written with 176 frames instead of 175 frames (i.e. 350/2)? Is it writing the last step of the previous run again? The frame at t=0 is always written to the .xtc, so you always have (nsteps/nstxout-compressed)+1 frames. -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] Adding HSD residue to AMBER ff99SB-ILDN
On 8/20/15 8:16 AM, Simone Bolognini wrote: Thank you for your answer! I did it and now gromacs throws me the following error: Atom HG1 in residue SER 2 was not found in rtp entry SER with 11 atoms while sorting atoms.. Any clue? Thank you very much. pdb2gmx -ignh -Justin Il giorno gio 20 ago 2015 alle ore 13:18 Justin Lemkul jalem...@vt.edu ha scritto: On 8/20/15 3:17 AM, Simone Bolognini wrote: Hi everyone, I have a .pdb file of the WW domain of human FIP35 protein extracted from an MD calculation obtained with AMBER ff99SB-ILDN and solvent type tip3. Now I need to obtain the topology out of it, but the .pdb contains a residue, namely HSD, which is not present in the Amber residue database. I looked at the source files and found out that CHARMM has it. In particular, this is what you can find in the CHARMM database: [ HSD ] [ atoms ] N NH1 -0.47 0 HN H 0.31 1 CA CT1 0.07 2 HA HB 0.09 3 CB CT2 -0.09 4 HB1 HA 0.09 5 HB2 HA 0.09 6 ND1 NR1 -0.36 7 HD1 H 0.32 8 CG CPH1 -0.05 9 CE1 CPH2 0.25 10 HE1 HR1 0.13 11 NE2 NR2 -0.70 12 CD2 CPH1 0.22 13 HD2 HR3 0.10 14 C C 0.51 15 O O -0.51 16 [ bonds ] CB CA CG CB ND1 CG CE1 ND1 NE2 CD2 N HN N CA C CA C +N CA HA CB HB1 CB HB2 ND1 HD1 CD2 HD2 CE1 HE1 O C CG CD2 CE1 NE2 [ impropers ] ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 ND1 CE1 CG HD1 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 N -C CA HN C CA +N O [ cmap ] -C N CA C +N Is there any possible way in which I can copy and paste this in the Amber database and hope it will work correctly? Thank you very much!!! No, you can't copy and paste, because then you're mixing force fields and that is bad practice. HSD is just delta-protonated HIS, which is already in AMBER. It's just called HID, so rename your coordinate files appropriately and you can generate the topology. -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. -- == 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] Broken protein chain: WARNING: Listed nonbonded interaction between particles ...
Hi all, I have a PDB file containing two proteins. One of the proteins has a long stretch of missing residues. When I try to energy-minimize it, I get the following: WARNING: Listed nonbonded interaction between particles 2897 and 2908 at distance 3f which is larger than the table limit 3f nm. Now, it turns out that atoms 2897 and 2908 belong to the residues between which the missing sequence lies. They are very far apart (because the missing stretch is quite long), so I don't think there should be any interaction between them. However, this WARNING seems to be saying that for some reason, the topology generated included an interaction between them, probably because it interpreted that since the two residues are consecutive in the PDB file, they are bonded (which they aren't, because of the missing residues). After trying some things, I realized that if I remove the option -chainsep id from pdb2gmx when I generate the topology, I don't get this warning. Instead, I get a bunch of topology files, each corresponding to a fragment of each chain, instead of a topology per chain. This is very hard to deal with, because, for example, if I want to make a position restrain on the backbone of each chain, I have to keep track of each fragment separately. Is there a way to fix the WARNING above without having to remove the option -chainsep id from pdb2gmx? Thanks. Best, cossio --- [http://5.cim.co.cu/cim.gif] -- 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] Broken protein chain: WARNING: Listed nonbonded interaction between particles ...
Hi, Yes, see pdbgmx -h about merge. Probably you want -merge interactive -chainsep id Mark On Thu, Aug 20, 2015 at 8:39 PM Jorge Fernandez de Cossio Diaz cos...@cim.sld.cu wrote: Hi all, I have a PDB file containing two proteins. One of the proteins has a long stretch of missing residues. When I try to energy-minimize it, I get the following: WARNING: Listed nonbonded interaction between particles 2897 and 2908 at distance 3f which is larger than the table limit 3f nm. Now, it turns out that atoms 2897 and 2908 belong to the residues between which the missing sequence lies. They are very far apart (because the missing stretch is quite long), so I don't think there should be any interaction between them. However, this WARNING seems to be saying that for some reason, the topology generated included an interaction between them, probably because it interpreted that since the two residues are consecutive in the PDB file, they are bonded (which they aren't, because of the missing residues). After trying some things, I realized that if I remove the option -chainsep id from pdb2gmx when I generate the topology, I don't get this warning. Instead, I get a bunch of topology files, each corresponding to a fragment of each chain, instead of a topology per chain. This is very hard to deal with, because, for example, if I want to make a position restrain on the backbone of each chain, I have to keep track of each fragment separately. Is there a way to fix the WARNING above without having to remove the option -chainsep id from pdb2gmx? Thanks. Best, cossio --- [http://5.cim.co.cu/cim.gif] -- 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] Problem compiling Gromacs 5.1
Thanks, Peter.
But , I mean I don’t know what line I should change to from line 52 of
cmake/FindPhinx.cmake to solve this error.
Leucer
2015/08/20 16:02、Kroon, P.C. p.c.kr...@rug.nl のメール：
Just use your favourite text editor.
Peter
On Thu, Aug 20, 2015 at 3:10 AM, atsutoshi0...@gmail.com wrote:
Line 52 of cmake/FindSphinx.cmake file is written below.
string(REGEX REPLACE Sphinx \\([^)]*\\) ([^ ]+) \\1
SPHINX_EXECUTABLE_VERSION ${SPHINX_VERSION_OUTPUT_VARIABLE})
Can you tell me how I can change the line?
Bests,
Leucer
2015/08/19 23:11、Mark Abraham mark.j.abra...@gmail.com のメッセージ:
Hi,
On Wed, Aug 19, 2015 at 3:49 PM 岡部篤俊 atsutoshi0...@gmail.com wrote:
Hi,
I am unable to compile Gromamcs 5.1 using the following cmake command.
cmake .. -DGMX_FFT_LIBRARY=fftpack
-DCMAKE_INSTALL_PREFIX=gromacs/gromacs-5.1 -DGMX_DOUBLE=off
-DGMX_THREAD_MPI=off -DGMX_MPI=on -DGMX_CPU_ACCELERATION=SSE4.1
Unrelated, but you now need to use -DGMX_SIMD=SSE4.1 to have the same
effect.
-DGMX_USE_RDTSCP=off
Then I got the error message.
Boost = 1.44 not found. Using minimal internal version. This may cause
trouble if you plan on compiling/linking other software that uses Boost
against GROMACS.
CMake Error at cmake/FindSphinx.cmake:52 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments total
to
command.
Call Stack (most recent call first):
docs/CMakeLists.txt:62 (find_package)
Could you advice what could be causing this error?
We try to find Sphinx in case people want to build the new documentation,
but it looks like some part of the detection isn't reliable enough. Can
you
please try changing line 52 of cmake/FindSphinx.cmake to read
string(REGEX REPLACE Sphinx \\([^)]*\\) ([^ ]+) \\1
SPHINX_EXECUTABLE_VERSION ${SPHINX_VERSION_OUTPUT_VARIABLE})
and let us know how you go?
Mark
I was able to compile Gromacs 5.0 using same cmake command….
Bests,
Leucer
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Re: [gmx-users] Problem compiling Gromacs 5.1
Hi,
You should change line 52 from what it is, to what I suggested - which
inserts quotation marks around one of the variable interpolations.
Mark
On Thu, Aug 20, 2015 at 2:43 PM 岡部篤俊 atsutoshi0...@gmail.com wrote:
Thanks, Peter.
But , I mean I don’t know what line I should change to from line 52 of
cmake/FindPhinx.cmake to solve this error.
Leucer
2015/08/20 16:02、Kroon, P.C. p.c.kr...@rug.nl のメール：
Just use your favourite text editor.
Peter
On Thu, Aug 20, 2015 at 3:10 AM, atsutoshi0...@gmail.com wrote:
Line 52 of cmake/FindSphinx.cmake file is written below.
string(REGEX REPLACE Sphinx \\([^)]*\\) ([^ ]+) \\1
SPHINX_EXECUTABLE_VERSION ${SPHINX_VERSION_OUTPUT_VARIABLE})
Can you tell me how I can change the line?
Bests,
Leucer
2015/08/19 23:11、Mark Abraham mark.j.abra...@gmail.com のメッセージ:
Hi,
On Wed, Aug 19, 2015 at 3:49 PM 岡部篤俊 atsutoshi0...@gmail.com wrote:
Hi,
I am unable to compile Gromamcs 5.1 using the following cmake
command.
cmake .. -DGMX_FFT_LIBRARY=fftpack
-DCMAKE_INSTALL_PREFIX=gromacs/gromacs-5.1 -DGMX_DOUBLE=off
-DGMX_THREAD_MPI=off -DGMX_MPI=on -DGMX_CPU_ACCELERATION=SSE4.1
Unrelated, but you now need to use -DGMX_SIMD=SSE4.1 to have the same
effect.
-DGMX_USE_RDTSCP=off
Then I got the error message.
Boost = 1.44 not found. Using minimal internal version. This may
cause
trouble if you plan on compiling/linking other software that uses
Boost
against GROMACS.
CMake Error at cmake/FindSphinx.cmake:52 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments
total
to
command.
Call Stack (most recent call first):
docs/CMakeLists.txt:62 (find_package)
Could you advice what could be causing this error?
We try to find Sphinx in case people want to build the new
documentation,
but it looks like some part of the detection isn't reliable enough. Can
you
please try changing line 52 of cmake/FindSphinx.cmake to read
string(REGEX REPLACE Sphinx \\([^)]*\\) ([^ ]+) \\1
SPHINX_EXECUTABLE_VERSION ${SPHINX_VERSION_OUTPUT_VARIABLE})
and let us know how you go?
Mark
I was able to compile Gromacs 5.0 using same cmake command….
Bests,
Leucer
--
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Re: [gmx-users] Problem compiling Gromacs 5.1
On 8/20/15 8:42 AM, 岡部篤俊 wrote:
Thanks, Peter.
But , I mean I don’t know what line I should change to from line 52 of
cmake/FindPhinx.cmake to solve this error.
Mark's message provided the corrected line. Just replace whatever is on line 52
with that.
-Justin
Leucer
2015/08/20 16:02、Kroon, P.C. p.c.kr...@rug.nl のメール：
Just use your favourite text editor.
Peter
On Thu, Aug 20, 2015 at 3:10 AM, atsutoshi0...@gmail.com wrote:
Line 52 of cmake/FindSphinx.cmake file is written below.
string(REGEX REPLACE Sphinx \\([^)]*\\) ([^ ]+) \\1
SPHINX_EXECUTABLE_VERSION ${SPHINX_VERSION_OUTPUT_VARIABLE})
Can you tell me how I can change the line?
Bests,
Leucer
2015/08/19 23:11、Mark Abraham mark.j.abra...@gmail.com のメッセージ:
Hi,
On Wed, Aug 19, 2015 at 3:49 PM 岡部篤俊 atsutoshi0...@gmail.com wrote:
Hi,
I am unable to compile Gromamcs 5.1 using the following cmake command.
cmake .. -DGMX_FFT_LIBRARY=fftpack
-DCMAKE_INSTALL_PREFIX=gromacs/gromacs-5.1 -DGMX_DOUBLE=off
-DGMX_THREAD_MPI=off -DGMX_MPI=on -DGMX_CPU_ACCELERATION=SSE4.1
Unrelated, but you now need to use -DGMX_SIMD=SSE4.1 to have the same
effect.
-DGMX_USE_RDTSCP=off
Then I got the error message.
Boost = 1.44 not found. Using minimal internal version. This may cause
trouble if you plan on compiling/linking other software that uses Boost
against GROMACS.
CMake Error at cmake/FindSphinx.cmake:52 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments total
to
command.
Call Stack (most recent call first):
docs/CMakeLists.txt:62 (find_package)
Could you advice what could be causing this error?
We try to find Sphinx in case people want to build the new documentation,
but it looks like some part of the detection isn't reliable enough. Can
you
please try changing line 52 of cmake/FindSphinx.cmake to read
string(REGEX REPLACE Sphinx \\([^)]*\\) ([^ ]+) \\1
SPHINX_EXECUTABLE_VERSION ${SPHINX_VERSION_OUTPUT_VARIABLE})
and let us know how you go?
Mark
I was able to compile Gromacs 5.0 using same cmake command….
Bests,
Leucer
--
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==
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
==
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Re: [gmx-users] Respect waters in crystallographic pdb file?
And what about genion? Suppose I have to add some ions to the system to neutralize, so I use the following command: genion -s S_ion.tpr -o S_sol.gro -p S_sol.top -nn 1 -nname CL SOL Is there a chance that this replaces one of the original crytallographic waters with the CL? Thanks. Best, cossio -- Message: 2 Date: Mon, 17 Aug 2015 14:14:28 -0400 From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Respect waters in crystallographic pdb file? Message-ID: 55d22484.9030...@vt.edu Content-Type: text/plain; charset=windows-1252; format=flowed They should be in the same place they always were (unless you've modified the box dimensions, in which case the coordinates of everything get changed). But genbox shouldn't delete waters that were already present. The crystallographic waters should always be the first ones written after e.g. the protein. -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 == On 8/17/15 1:42 PM, Jorge Fernandez de Cossio Diaz wrote: Hi all, I have a crystallographic PDB file which comes some waters molecules. I want to run an MD simulation which includes those water molecules. After generating the topology file (which includes the waters) and defining the box shape, I fill the box with solvent using genbox. At this point it becomes impossible to track down visually where the water molecules are. My question is if the file that genbox outputs still contains the crystallographic water molecules? Or are they replaced by the molecules added by genbox? Thanks in --- [http://5.cim.co.cu/cim.gif] -- 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] Respect waters in crystallographic pdb file?
On 8/20/15 10:06 AM, Jorge Fernandez de Cossio Diaz wrote: And what about genion? Suppose I have to add some ions to the system to neutralize, so I use the following command: genion -s S_ion.tpr -o S_sol.gro -p S_sol.top -nn 1 -nname CL SOL Is there a chance that this replaces one of the original crytallographic waters with the CL? There's always a chance; it's random. It's easy to check and if you get an undesired result, just change the value of -seed. Or distinguish the crystal waters as some other [moleculetype] name, which requires some topology hacking. -Justin Thanks. Best, cossio -- Message: 2 Date: Mon, 17 Aug 2015 14:14:28 -0400 From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Respect waters in crystallographic pdb file? Message-ID: 55d22484.9030...@vt.edu Content-Type: text/plain; charset=windows-1252; format=flowed They should be in the same place they always were (unless you've modified the box dimensions, in which case the coordinates of everything get changed). But genbox shouldn't delete waters that were already present. The crystallographic waters should always be the first ones written after e.g. the protein. -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 == On 8/17/15 1:42 PM, Jorge Fernandez de Cossio Diaz wrote: Hi all, I have a crystallographic PDB file which comes some waters molecules. I want to run an MD simulation which includes those water molecules. After generating the topology file (which includes the waters) and defining the box shape, I fill the box with solvent using genbox. At this point it becomes impossible to track down visually where the water molecules are. My question is if the file that genbox outputs still contains the crystallographic water molecules? Or are they replaced by the molecules added by genbox? Thanks in --- [http://5.cim.co.cu/cim.gif] -- == 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] inversion potential
Hi, Dear gromacs usersI want to define some bond parameters within opls-aa force field, which are taken from a paper. I know how to define nonbonded parameters as well as bonds and angles and dihedrals. But I don't know how to define a so-called inversion potential and the paper is vague on this. The paper reads: u_inversion(theta_ijk-theta_0)=K1(theta_ijk-theta_0)+K2(theta_ijk-theta_0)^2inversion theta0(deg) K1(kcal/mol/rad) K2(kcal/mol/rad^2) C1 360 -60 30 The only way to define such a form of potential in gromacs, as I found out from the manual, is to use a quartic angle (please see table 5.5 of the manual). The manual says that one has to specify 3 atoms to define such an angle potential. However, the paper has specified only one atom (C1)!! Although it has not clarified, it seems that the paper is using this potential to avoid the rotation of the mentioned atom (due to theta0=360 deg). Does anyone happen to know the answers to the following questions:1- What is this inversion potential used for?2-How can I implement it in Gromacs?I appreciate any kind comments on this issue.Thanks.Nima Azar -- 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] trjconv -dt issue
Thanks for your explanation, Mark. Concerning energy files and eneconv: - I will try double-precision eneconv, as I don't mind larger files. - In reply to the advice to reset the time of the energy files: how to do it? eneconv has no option for this, although the help states: With one file specified for -f: Reads one energy file and writes another, applying the -dt, -offset, -t0 and -settime options and converting to a different format if necessary (indicated by file extentions). Strangely, the -t0 option does not exist in eneconv (GROMACS 4.6.5) and if I try nevertheless, it states Invalid command line argument: -t0. Is that an error in the help or was the option just forgotten for the command line parsing of eneconv? - The eneconv -offset option seems to do nothing for me (or I looked at the wrong spot). What does it do and how is supposed to work? - And last: eneconv has, in contrast to trjconv, no -skip option which would allow for using every nth frame instead of choosing by time. Is that intended? Right now, it could be helpful for me, so I would like to state my request for it ;-) Concerning xtc files: Obviously, the data types storing the step counter as well as the timestamp are too small for my data. The step counter overflows quite rapidly, but also the time only works for ps steps up to 1.6777216E7 (i.e. ~16.777mus). Going further, only even numbers are stored. This gives a nasty number of Timesteps at t=... don't match messages when using gmxcheck to see if everything went alright, obscuring real errors that may be in between. Is there any chance of saving the correct times in the trajectory file (like using double-precision like for eneconv) or do I have to take care of this separately? Or is there some other format I could use to save the data efficiently? Thanks a lot, Matthias On 08/20/2015 12:56 PM, Mark Abraham wrote: Hi, This is indeed problematic. The .edr format (and its tools) are designed with limitations that were not really a problem 10 years ago. One of the limitations is that the time itself is stored in the same precision as the simulation data, and this starts to lose precision as the simulation proceeds into the millions of MD steps. I think your practical course is to keep the simulation in the chunks that you already have, and do your subsampling from them. You may get a better result if you pre-process each chunk to start from zero time (or making smaller chunks if you need to). This will help by keeping the side of the stride closer to the absolute value of the time. Another alternative is to pre-process the chunks with a double-precision eneconv, which will write the times in double precision. That won't help if they're stored wrongly in the first place, but may help you handle some longer trajectory (at cost of more disk space). Mark On Wed, Aug 19, 2015 at 11:50 PM Matthias Ernst matthias.er...@physik.uni-freiburg.de wrote: Hello, I have a quite long continuous trajectory coming from several initial input pieces (cluster crashed...) that I want to downsample, as a start from 0.5ps timestep in the source files to just 1ps and later bigger timesteps. Using the -dt option of trjconv (GROMACS 4.6.5.), there seem to be rounding issues which leads to times at .5ps being written from some timestamp on (4.1943e+06). Is this a known behaviour? Related to this, what does the following sentence in the help for trjconv -dt mean: This option relies on the accuracy of the times in your input trajectory, so if these are inaccurate use the -timestep option to modify the time (this can be done simultaneously). How can I change the input timestep to get a proper output of output frames? I tried to use -timestep 1 it to my trajectory with 0.5ps timestep and it seems to produce correct timestamps in 1ps steps in the output file but the coordinates still are those of the initial frames with the 0.5ps timestamps, meaning it just relabels the timestamps of the frames. Using -timestep 0.5 -dt 1 together does not change the result compared to -dt 1 only. If I rather use the -t0 0 option, I can reset the time of the first frame and then, it looks like it writes the correct 1ps stepped frames with 1ps timestamps, but starting at time 0. As I have several trajectory pieces from a continuous timeseries to concatenate, I would have to run trjconv once more just to correct and reset the time to its initial value, which means a lot of unnecessary data transfer, especially in the case of long trajectories. Is this really necessary or is there another way to get a proper downsampling? I know I can use the -skip 2 option but e.g. not for eneconv which only supports -dt and has the same issues. Further, just using -skip 2 is not possible if some input files are at 0.5ps, but some other already at 1ps time steps. Thank you for your help, Matthias -- Progress... http://www.phdcomics.com/comics/archive.php?comicid=1611 --
Re: [gmx-users] trjconv -dt issue
Hi, On Thu, Aug 20, 2015 at 4:00 PM Matthias Ernst matthias.er...@physik.uni-freiburg.de wrote: Thanks for your explanation, Mark. Concerning energy files and eneconv: - I will try double-precision eneconv, as I don't mind larger files. - In reply to the advice to reset the time of the energy files: how to do it? I intended you to try eneconv -settime 0 for each file. eneconv has no option for this, although the help states: With one file specified for -f: Reads one energy file and writes another, applying the -dt, -offset, -t0 and -settime options and converting to a different format if necessary (indicated by file extentions). Strangely, the -t0 option does not exist in eneconv (GROMACS 4.6.5) and if I try nevertheless, it states Invalid command line argument: -t0. Is that an error in the help or was the option just forgotten for the command line parsing of eneconv? Looks like it :-( - The eneconv -offset option seems to do nothing for me (or I looked at the wrong spot). What does it do and how is supposed to work? See doc string for -dt (so not useful for you) - And last: eneconv has, in contrast to trjconv, no -skip option which would allow for using every nth frame instead of choosing by time. Is that intended? Right now, it could be helpful for me, so I would like to state my request for it ;-) Fair enough. My plan to fix such issues in the future is to move all energy writing to the TNG format introduced in 5.0, and now there is no need for two separate tools to do the same thing (and neither doing it very well). A further option for you is to use gmxdump to get the data in a text format - where the step number will be clear and potentially useful. That's a one-way trip, however - you won't get the data back into .edr format. There are some third-party MD analysis packages that might help, I have no idea. Concerning xtc files: Obviously, the data types storing the step counter as well as the timestamp are too small for my data. The step counter overflows quite rapidly, I think we changed the step counter to a 64-bit integer before GROMACS 4.5. Doubtless some places print it badly, but I don't think you're doing 10^19 steps. but also the time only works for ps steps up to 1.6777216E7 (i.e. ~16.777mus). Going further, only even numbers are stored. This gives a nasty number of Timesteps at t=... don't match messages when using gmxcheck to see if everything went alright, obscuring real errors that may be in between. Yep. This gear is fast becoming out of date. Is there any chance of saving the correct times in the trajectory file (like using double-precision like for eneconv) or do I have to take care of this separately? Or is there some other format I could use to save the data efficiently? Unless you run mdrun in double precision, the step number is the only reliable thing, unfortunately. Internally, the magnitude of the step number and time is only used for trivia, and clearly there are a number of things that could be improved about how we handle writing and post-processing data. Mark Thanks a lot, Matthias On 08/20/2015 12:56 PM, Mark Abraham wrote: Hi, This is indeed problematic. The .edr format (and its tools) are designed with limitations that were not really a problem 10 years ago. One of the limitations is that the time itself is stored in the same precision as the simulation data, and this starts to lose precision as the simulation proceeds into the millions of MD steps. I think your practical course is to keep the simulation in the chunks that you already have, and do your subsampling from them. You may get a better result if you pre-process each chunk to start from zero time (or making smaller chunks if you need to). This will help by keeping the side of the stride closer to the absolute value of the time. Another alternative is to pre-process the chunks with a double-precision eneconv, which will write the times in double precision. That won't help if they're stored wrongly in the first place, but may help you handle some longer trajectory (at cost of more disk space). Mark On Wed, Aug 19, 2015 at 11:50 PM Matthias Ernst matthias.er...@physik.uni-freiburg.de wrote: Hello, I have a quite long continuous trajectory coming from several initial input pieces (cluster crashed...) that I want to downsample, as a start from 0.5ps timestep in the source files to just 1ps and later bigger timesteps. Using the -dt option of trjconv (GROMACS 4.6.5.), there seem to be rounding issues which leads to times at .5ps being written from some timestamp on (4.1943e+06). Is this a known behaviour? Related to this, what does the following sentence in the help for trjconv -dt mean: This option relies on the accuracy of the times in your input trajectory, so if these are inaccurate use the -timestep option to modify the time (this can be done simultaneously).
Re: [gmx-users] Error while configuring gmx-3.3.1
Thanks Mark, It worked. grompp working fine now. regards, Padmani On Thu, Aug 20, 2015 at 4:14 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Apparently the 3.3.1 install isn't working well for you. You can use cp -R gromacs-3.3.1/share/top/* /usr/local/gromacs/share/top/ which is a standard unix command. Mark On Thu, Aug 20, 2015 at 5:52 AM Padmani Sandhu padmanisandh...@gmail.com wrote: Hello Justin, I have copied both the .itp files which were giving error in to /usr/local/gromacs/share/top using command: sudo cp BH4_oplsaa.itp /usr/local/gromacs/share/top sudo cp ffoplsaabon.itp /usr/local/gromacs/share/top and now grompp worked. Please can you suggest me any solution so that all the files in *gromacs-3.3.1/share/top *can be copied to */usr/local/gromacs/share/top.* Thanks Padmani On Wed, Aug 19, 2015 at 5:42 PM, Padmani Sandhu padmanisandh...@gmail.com wrote: 1. I am using it with CPMD as they have mentioned this version of gromacs only. 2. The top-level force fields are not included as they are not present in /usr/local/gromacs/share/top/ file for eg. BH4_oplsaa.itp, however its there in the gmx-3.3.1_qmmm-1.3.2/share/top folder. 3. There is no problem with topology, its working fine with gromacs-4.5.6 and later versions. Thanks Padmani On Wed, Aug 19, 2015 at 5:32 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/19/15 7:58 AM, Padmani Sandhu wrote: Hello everyone, I am trying to install gmx-3.3.1 on ubuntu 14.04. I have compiled it using following commands: Any reason you're using wildly outdated software? ./configure make sudo make install *However the program was installed but while running grommp, it was terminated with an error :* checking input for internal consistency... calling cpp... In file included from /usr/local/gromacs/share/top/ffoplsaa.itp:23:0, from topol.top:11: /usr/local/gromacs/share/top/ffoplsaabon.itp:2692:26: fatal error: BH4_oplsaa.itp: No such file or directory #include BH4_oplsaa.itp ^ compilation terminated. You probably shouldn't be #including files in top-level force field files. cpp exit code: 256 Tried to execute: 'cpp -I/usr/local/gromacs/share/top topol.top gromppVUW784' The 'cpp' command is defined in the .mdp file processing topology... processing coordinates... --- Program grompp, VERSION 3.3.1 Source code file: grompp.c, line: 448 Fatal error: number of coordinates in coordinate file (conf_solv.gro, 317253) does not match topology (topol.top, 0) Your topology is totally wrong or misformatted. *I had an error while running ./configure that might be causing this problem* configure: creating ./config.status config.status: creating Makefile config.status: WARNING: Makefile.in seems to ignore the --datarootdir setting config.status: creating src/Makefile config.status: WARNING: src/Makefile.in seems to ignore the --datarootdir setting This is not related. -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. -- *Padmani sandhu* *Research Scholar,* *Center for Computational Biology and Bioinformatics,* *Central University of Himachal Pradesh,* *Temporary Academic Block, Shahpur * *Pin 176206, District Kangra,* *Himachal Pradesh, India* -- *Padmani sandhu* *Research Scholar,* *Center for Computational Biology and Bioinformatics,* *Central University of Himachal Pradesh,* *Temporary Academic Block, Shahpur * *Pin 176206, District Kangra,* *Himachal Pradesh, India* -- 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
[gmx-users] No Checkpoint File generated
Dear All, I am doing a md simulation for a system consisting of protein with 1.5ns thick water shell. The whole system is simulated in vacuum. I turn of PBC and cutoffs for nonbond interactions. Now, the simulation runs well, but no checkpoint file is output. Does anyone know the issue? The parameters in .mdp file is appended. Thanks in advance. Chunlei * define = -DPOSRES -DFPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 25 ; 2 * 25 000 = 50 ps dt = 0.002 ; 2 fs ; Output control nstxout = 0 ; save coordinates every 1 ps nstvout = 0 ; save velocities every 1 ps nstxtcout = 500 ; save compressed coordinates very 1 ps nstenergy = 500 ; save energies every 1 ps nstlog = 500 ; update log file every 1 ps ; Bond parameters continuation = no ; continue from nvt run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = simple ; search neighboring grid cels nstlist = 0 ; 10 fs rlist = 0 ; short-range neighborlist cutoff (in nm) rcoulomb = 0 ; short-range electrostatic cutoff (in nm) rvdw = 0 ; short-range van der Waals cutoff (in nm) vdwtype = cut-off ; twin-range cut-off for vdw interation coulombtype = cut-off ; Particle Mesh Ewald for long-range electrostatics ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein SOL RWW ; two coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = 300 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = no ; 3-D PBC comm_mode = ANGULAR nstcomm = 1 -- 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] Broken protein chain: WARNING: Listed nonbonded
Note that I am adding position restrains to fix all the termini of the incomplete fragments. Shouldn't that take care of the missing residues? -- Message: 5 Date: Thu, 20 Aug 2015 20:29:42 + From: Jorge Fernandez de Cossio Diaz cos...@cim.sld.cu To: gromacs.org_gmx-users@maillist.sys.kth.se gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded interaction between particles ... Message-ID: fcd5150195922740996c04d9f8a6dfbb52c4c...@cimex2010mb1.cim.sld.cu Content-Type: text/plain; charset=us-ascii Tried using -merge interactive -chainsep id on pdb2gmx, but I still get the same WARNING: WARNING: Listed nonbonded interaction between particles 2897 and 2908 at distance 3f which is larger than the table limit 3f nm. The energy minimization step prints this as a warning and proceeds, but when I try to equilibrate the system later, the warning becomes an error and it doesn't let me proceed, so this seems to be important. Also, it doesn't make sense to me that 2897 and 2908 are interacting, because even though they are consecutive (because of missing residues), they are very far apart in space. So why is it that when I put the fragments into the same chain, the topology creates this spurious interaction? -- Message: 4 Date: Thu, 20 Aug 2015 19:00:29 + From: Mark Abraham mark.j.abra...@gmail.com To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded interaction between particles ... Message-ID: CAMNuMARXoFeT_HN0J57y2pt=gzatnzgb+11asgpm6dxvyq3...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Hi, Yes, see pdbgmx -h about merge. Probably you want -merge interactive -chainsep id Mark On Thu, Aug 20, 2015 at 8:39 PM Jorge Fernandez de Cossio Diaz cos...@cim.sld.cu wrote: Hi all, I have a PDB file containing two proteins. One of the proteins has a long stretch of missing residues. When I try to energy-minimize it, I get the following: WARNING: Listed nonbonded interaction between particles 2897 and 2908 at distance 3f which is larger than the table limit 3f nm. Now, it turns out that atoms 2897 and 2908 belong to the residues between which the missing sequence lies. They are very far apart (because the missing stretch is quite long), so I don't think there should be any interaction between them. However, this WARNING seems to be saying that for some reason, the topology generated included an interaction between them, probably because it interpreted that since the two residues are consecutive in the PDB file, they are bonded (which they aren't, because of the missing residues). After trying some things, I realized that if I remove the option -chainsep id from pdb2gmx when I generate the topology, I don't get this warning. Instead, I get a bunch of topology files, each corresponding to a fragment of each chain, instead of a topology per chain. This is very hard to deal with, because, for example, if I want to make a position restrain on the backbone of each chain, I have to keep track of each fragment separately. Is there a way to fix the WARNING above without having to remove the option -chainsep id from pdb2gmx? Thanks. Best, cossio --- --- [http://5.cim.co.cu/cim.gif] -- Message: 6 Date: Thu, 20 Aug 2015 16:40:27 -0400 From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded interaction between particles ... Message-ID: 55d63b3b.6040...@vt.edu Content-Type: text/plain; charset=windows-1252; format=flowed On 8/20/15 4:29 PM, Jorge Fernandez de Cossio Diaz wrote: Tried using -merge interactive -chainsep id on pdb2gmx, but I still get the same WARNING: WARNING: Listed nonbonded interaction between particles 2897 and 2908 at distance 3f which is larger than the table limit 3f nm. The energy minimization step prints this as a warning and proceeds, but when I try to equilibrate the system later, the warning becomes an error and it doesn't let me proceed, so this seems to be important. Also, it doesn't make sense to me that 2897 and 2908 are interacting, because even though they are consecutive (because of missing residues), they are very far apart in space. So why is it that when I put the fragments into the same chain, the topology creates this spurious interaction? Because you're ignoring something physically relevant - you have missing residues! pdb2gmx certainly gave long bond warnings when you produced the topology. You need to model in the missing residues, otherwise the structure is useless to you. -Justin
Re: [gmx-users] Incorrect number of parameters - found 3, expected 1 or 1 for Polarization.
On 8/20/15 4:01 PM, 折晓会 wrote: Thank you professor Justin! I solved this error with your suggestion. When I use mdrun -rerun to calculate the local pressure, another error occurs: Fatal error: Rerun trajectory frame step 60 time 600.00 has too small box dimensions What does this mean? It means your box is too small. What are the box dimensions in that frame, and what are the cutoffs you are using? -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] What's the point of adding ions to neutralize the system?
On 8/20/15 4:15 PM, Victor Rosas Garcia wrote: You said it yourself: to neutralize the net charge of the system. Great answer: you neutralize the system in order to neutralize the system :) Since the ion added is usually very far away from the protein (or molecule of interest), I don't see how it can affect the results of the molecular dynamics simulation. So why is it so important to add ions to neutralize the net-charge of the system? One effect is practical - in the absence of a net-neutral system, PME applies a neutralizing background charge, which for a homogeneous medium, is an adequate approximation. But this is a very bad approximation in many other cases. There are even relevant inhomogeneities at protein surfaces, though the effects are not as profound as, say, in a membrane system. Second point - life exists in salt. We like to model things that are biologically relevant. Third and final point - it is fundamentally incorrect to assume that there will be no effect of the ions. DNA dynamics are exquisitely sensitive to ionic concentration, for instance (though additive models are not nearly as responsive as polarizable ones, there are some effects). Protein salt bridges are affected by ionic concentration, even if the interactions are not direct, there is a change in ionic environment within a hydration shell or two and that will affect dynamics. And even if ions are far away from the solute to start, they don't stay there... a-Justin --- [http://5.cim.co.cu/cim.gif] -- 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. -- == 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] Incorrect number of parameters - found 3, expected 1 or 1 for Polarization.
Thank you professor Justin! I solved this error with your suggestion. When I use mdrun -rerun to calculate the local pressure, another error occurs: Fatal error: Rerun trajectory frame step 60 time 600.00 has too small box dimensions What does this mean? Best wishes, Xiaohui Date: Thu, 20 Aug 2015 13:05:27 -0400 From: jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Incorrect number of parameters - found 3, expected 1 or 1 for Polarization. On 8/20/15 1:03 PM, 折晓会 wrote: Dear all, I used Gromacs 5.0.5 to generate a trajectory of polarizable water system with SWM4-NDP model, and then tried to use a custom version Gromacs 4.5.5 to calculate local pressure of the system. When I generate the .tpr file with Gromacs 4.5.5, an error coccurs: Fatal error: Incorrect number of parameters - found 3, expected 1 or 1 for Polarization. What does this mean? How should I solve this problem? This means that you have too many parameters on some line related to the [polarization] directive. Isotropic polarization takes one value (alpha), so that's all that is allowed. -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] Broken protein chain: WARNING: Listed nonbonded interaction between particles ...
Tried using -merge interactive -chainsep id on pdb2gmx, but I still get the same WARNING: WARNING: Listed nonbonded interaction between particles 2897 and 2908 at distance 3f which is larger than the table limit 3f nm. The energy minimization step prints this as a warning and proceeds, but when I try to equilibrate the system later, the warning becomes an error and it doesn't let me proceed, so this seems to be important. Also, it doesn't make sense to me that 2897 and 2908 are interacting, because even though they are consecutive (because of missing residues), they are very far apart in space. So why is it that when I put the fragments into the same chain, the topology creates this spurious interaction? -- Message: 4 Date: Thu, 20 Aug 2015 19:00:29 + From: Mark Abraham mark.j.abra...@gmail.com To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded interaction between particles ... Message-ID: CAMNuMARXoFeT_HN0J57y2pt=gzatnzgb+11asgpm6dxvyq3...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Hi, Yes, see pdbgmx -h about merge. Probably you want -merge interactive -chainsep id Mark On Thu, Aug 20, 2015 at 8:39 PM Jorge Fernandez de Cossio Diaz cos...@cim.sld.cu wrote: Hi all, I have a PDB file containing two proteins. One of the proteins has a long stretch of missing residues. When I try to energy-minimize it, I get the following: WARNING: Listed nonbonded interaction between particles 2897 and 2908 at distance 3f which is larger than the table limit 3f nm. Now, it turns out that atoms 2897 and 2908 belong to the residues between which the missing sequence lies. They are very far apart (because the missing stretch is quite long), so I don't think there should be any interaction between them. However, this WARNING seems to be saying that for some reason, the topology generated included an interaction between them, probably because it interpreted that since the two residues are consecutive in the PDB file, they are bonded (which they aren't, because of the missing residues). After trying some things, I realized that if I remove the option -chainsep id from pdb2gmx when I generate the topology, I don't get this warning. Instead, I get a bunch of topology files, each corresponding to a fragment of each chain, instead of a topology per chain. This is very hard to deal with, because, for example, if I want to make a position restrain on the backbone of each chain, I have to keep track of each fragment separately. Is there a way to fix the WARNING above without having to remove the option -chainsep id from pdb2gmx? Thanks. Best, cossio --- --- [http://5.cim.co.cu/cim.gif] -- 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] High load imbalance: 31.8%
Hi Mark, Many thanks for looking into this. One of the log files (the job hasn’t finished running) is here: https://www.dropbox.com/s/zwrro54yni2uxtn/umb_3_umb.log?dl=0 The system is a soluble collagenase in water with a collagen substrate and two zinc co-factors. There are 287562 atoms in the system. Please let me know if you need to know anything else. Thanks! Anthony On 20/08/2015 11:39, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, In cases like this, it's good to describe what's in your simulation, and share the full .log file on a file-sharing service, so we can see both the things mdrun reports early and late. Mark On Thu, Aug 20, 2015 at 8:22 AM Nash, Anthony a.n...@ucl.ac.uk wrote: Hi all, I appear to have a very high load imbalance on some of my runs. Values starting from approx. 7% up to 31.8% with reported vol min/aver of around 0.6 (I haven¹t found one under half yet). When I look through the .log file at the start of the run I see: Initializing Domain Decomposition on 8 ranks Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 0.514 nm, LJ-14, atoms 3116 3123 multi-body bonded interactions: 0.429 nm, Proper Dih., atoms 3116 3123 Minimum cell size due to bonded interactions: 0.472 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.862 nm Estimated maximum distance required for P-LINCS: 0.862 nm This distance will limit the DD cell size, you can override this with -rcon Using 0 separate PME ranks, as there are too few total ranks for efficient splitting Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 8 cells with a minimum initial size of 1.077 nm The maximum allowed number of cells is: X 12 Y 12 Z 12 Domain decomposition grid 4 x 2 x 1, separate PME ranks 0 PME domain decomposition: 4 x 2 x 1 Domain decomposition rank 0, coordinates 0 0 0 Using 8 MPI processes Using 1 OpenMP thread per MPI process Having a quick look through the documentation and I see that I should consider implementing the verlet cut-off (which I am) and adjust the number of PME nodes/cut-off and PME grid spacing. Would this simply be a case of throwing more cores at the simulation or must I play around with P-LINCS parameters? Thanks Anthony -- 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] High load imbalance: 31.8%
Hi, You're not pinning threads and it seems that you're running on a large SMP machine! Assuming that the 512 threads reported (line 91) is correct that's a 32 socket SMP machine, perhaps an SGI UV? In any case Xeon E5-4xxx is typically deployed in 4-8 socket installations, so your 8 threads will be floating around on a number of CPUs which ruins your performance - and likely contributes to the varying and large load imbalance. My advice: - don't ignore notes/warnings issued by mdrun (line 366, should be on the standard out too), we put quite some though into spamming users only when relevant :) - pin mdrun and/or its threads either with -pin on (and -pinoffset if needed) or with whatever tools your admins provide/recommend [Extras: consider using FFTW even with the Intel compilers it's often faster for our small FFTs than MKL; and GNU iso Intel compiler is often faster too.] Fixing the above issues should not only reduce imbalance but most likely also allow you to gain quite some simulation performance! Let us know if it worked. Cheers, -- Szilárd On Thu, Aug 20, 2015 at 5:08 PM, Nash, Anthony a.n...@ucl.ac.uk wrote: Hi Mark, Many thanks for looking into this. One of the log files (the job hasn’t finished running) is here: https://www.dropbox.com/s/zwrro54yni2uxtn/umb_3_umb.log?dl=0 The system is a soluble collagenase in water with a collagen substrate and two zinc co-factors. There are 287562 atoms in the system. Please let me know if you need to know anything else. Thanks! Anthony On 20/08/2015 11:39, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, In cases like this, it's good to describe what's in your simulation, and share the full .log file on a file-sharing service, so we can see both the things mdrun reports early and late. Mark On Thu, Aug 20, 2015 at 8:22 AM Nash, Anthony a.n...@ucl.ac.uk wrote: Hi all, I appear to have a very high load imbalance on some of my runs. Values starting from approx. 7% up to 31.8% with reported vol min/aver of around 0.6 (I haven¹t found one under half yet). When I look through the .log file at the start of the run I see: Initializing Domain Decomposition on 8 ranks Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 0.514 nm, LJ-14, atoms 3116 3123 multi-body bonded interactions: 0.429 nm, Proper Dih., atoms 3116 3123 Minimum cell size due to bonded interactions: 0.472 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.862 nm Estimated maximum distance required for P-LINCS: 0.862 nm This distance will limit the DD cell size, you can override this with -rcon Using 0 separate PME ranks, as there are too few total ranks for efficient splitting Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 8 cells with a minimum initial size of 1.077 nm The maximum allowed number of cells is: X 12 Y 12 Z 12 Domain decomposition grid 4 x 2 x 1, separate PME ranks 0 PME domain decomposition: 4 x 2 x 1 Domain decomposition rank 0, coordinates 0 0 0 Using 8 MPI processes Using 1 OpenMP thread per MPI process Having a quick look through the documentation and I see that I should consider implementing the verlet cut-off (which I am) and adjust the number of PME nodes/cut-off and PME grid spacing. Would this simply be a case of throwing more cores at the simulation or must I play around with P-LINCS parameters? Thanks Anthony -- 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
[gmx-users] What's the point of adding ions to neutralize the system?
Since the ion added is usually very far away from the protein (or molecule of interest), I don't see how it can affect the results of the molecular dynamics simulation. So why is it so important to add ions to neutralize the net-charge of the system? --- [http://5.cim.co.cu/cim.gif] -- 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] AIX XLC Gromacs-5.1-rc1. Undefined reference. Underscore issue.
Hello Mark! Thank you for your advice! I'm now using Gromacs-5.1. I've added -DGMX_BUILD_MDRUN_ONLY=ON on the previous cmake configuration. Here's my cmake and error log now: export TPREFIX=/home/ibm/softwares/gromacs/xlc/vsx/omp1/flagO0/ export flags1=-qnoinline -O0 -qsmp=omp export blaslapackflags=-L/usr/lib -lessl -L/opt/ibm/xlf/15.1.2/lib/ -lxlf90 -lxlf90_t -L/opt/ibm/xlsmp/4.1.2/lib -lxlomp_ser cmake .. -DGMX_MPI=on -DGMX_DOUBLE=off -DCMAKE_INSTALL_PREFIX=$TPREFIX -DBUILD_SHARED_LIBS=OFF -DGMX_FFT_LIBRARY=essl -DGMX_OPENMP=on -DCMAKE_VERBOSE_MAKEFILE=on -DGMX_GPU=off -DGMX_EXTERNAL_LAPACK=ON -DGMX_EXTERNAL_BLAS=ON -DGMX_BLAS_USER=$blaslapackflags -DGMX_LAPACK_USER=$blaslapackflags -DCMAKE_CXX_FLAGS=$flags1 -DCMAKE_C_FLAGS=$flags1 -DGMX_THREAD_MPI=off -DGMX_SIMD=IBM_VSX -DCMAKE_C_COMPILER=mpixlc -DCMAKE_CXX_COMPILER=mpixlc++ -DFFT_LINKER_FLAGS= -DLINEAR_ALGEBRA_LIBRARIES= -DCOVERAGE_EXTRA_FLAGS= -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_SHARED_LINKER_FLAGS=-qnoextname -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BUILD_SHARED_EXE=OFF - Error log: Linking CXX executable ../../bin/mdrun_mpi cd /home/ibm/crash/2gromacs-5.1-agosto/gromacs-5.1/single/src/programs /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun.dir/link.txt --verbose=1 /usr/bin/mpixlc++-qarch=auto -qaltivec -std=c++0x -qnoinline -O0 -qsmp=omp -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -O3 -DNDEBUG CMakeFiles/mdrun.dir/mdrun_main.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/membed.c.o CMakeFiles/mdrun_objlib.dir/mdrun/resource-division.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/runner.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/md.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/repl_ex.cpp.o -o ../../bin/mdrun_mpi -rdynamic ../../lib/libgromacs_mdrun_mpi.a -lrt /opt/ibmmath/essl/5.3/FFTW3/src/lib64/libfftw3_essl.a -L/usr/lib -lessl -L/opt/ibm/xlf/15.1.2/lib/ -lxlf90 -lxlf90_t -L/opt/ibm/xlsmp/4.1.2/lib -lxlomp_ser ../../lib/libgromacs_mdrun_mpi.a(copyrite.cpp.o): In function `gmx_print_version_info(_IO_FILE*)': copyrite.cpp:(.text+0x1310): undefined reference to `gmx_fft_get_version_info' copyrite.cpp:(.text+0x15f4): undefined reference to `gmx_fft_get_version_info' ../../lib/libgromacs_mdrun_mpi.a(fft.cpp.o): In function `gmx_fft_init_many_1d': fft.cpp:(.text+0x98): undefined reference to `gmx_fft_init_1d' ../../lib/libgromacs_mdrun_mpi.a(fft.cpp.o): In function `gmx_fft_init_many_1d_real': fft.cpp:(.text+0x1a8): undefined reference to `gmx_fft_init_1d_real' ../../lib/libgromacs_mdrun_mpi.a(fft.cpp.o): In function `gmx_many_fft_destroy': fft.cpp:(.text+0x300): undefined reference to `gmx_fft_destroy' ../../lib/libgromacs_mdrun_mpi.a(fft.cpp.o): In function `gmx_fft_many_1d_real$AF7_4': fft.cpp:(.text+0xfd0): undefined reference to `gmx_fft_1d_real' ../../lib/libgromacs_mdrun_mpi.a(fft.cpp.o): In function `gmx_fft_many_1d$AF8_3': fft.cpp:(.text+0x10c0): undefined reference to `gmx_fft_1d' Thanks in advance! Carlos. On Thu, Aug 20, 2015 at 7:42 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, GROMACS 5.1 is out, please don't install 5.1-rc1 any more. There's a little bit of advice about using custom linear algebra libraries at http://manual.gromacs.org/documentation/5.1/install-guide/index.html#linear-algebra-libraries but you don't need to bother with such libraries unless you know mdrun will be used to do normal-mode analysis or something. You might still run into problems - if so, we'll want to know how you ran cmake in the first place. Mark On Thu, Aug 20, 2015 at 1:20 AM Carlos Aguni sorla...@gmail.com wrote: Helo guys! I'm trying to compile Gromacs-5.1-rc1 with XLC 13.1.2 ESSL 5.3 and I'm facing an undefined reference error. Here's what I got: $ cd /home/ibm/crash/gromacs-agosto/2/gromacs-5.1-rc1/single/share/template /usr/bin/cmake -E cmake_link_script CMakeFiles/template.dir/link.txt --verbose=1 $ /usr/bin/mpixlc++-qarch=auto -qaltivec -std=c++0x -qnoinline -O0 -qsmp=omp -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -O3 -DNDEBUG -qextname CMakeFiles/template.dir/template.cpp.o -o ../../bin/template -rdynamic ../../lib/libgromacs_mpi.so.1.0.0 -ldl -lrt -lessl -L/usr/lib -lessl -L/opt/ibm/xlf/15.1.2/lib/ -lxlf90 -lxlf90_t -Wl,-rpath,\$ORIGIN/../lib /opt/ibm/xlC/13.1.2/bin/.orig/xlc++: warning: 1501-218 file ../../lib/libgromacs_mpi.so.1.0.0 contains an incorrect file suffix ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `dlaev2_' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `dorm2r_' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `gmx_fft_init_1d_real' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `dlascl_' ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `slaev2_'
Re: [gmx-users] AIX XLC Gromacs-5.1-rc1. Undefined reference. Underscore issue.
Hi, Using -DGMX_FFT_LIBRARY=essl is not meaningful (per install guide), and frankly it's a build-system bug if it doesn't give a fatal error :-) That's likely the reason for the undefined symbols for the GROMACS wrapper functions that call the underlying FFT library (and that the conditional compilation can mysteriously fail like this is also a bug). If essl has a magic FFTW compatibility mode, you should use -DGMX_FFT_LIBRARY=fftw3 and set -DCMAKE_PREFIX_PATH=/path/to/essl/fftw/dir/ so that the essl fftw library gets found before any other FFTW library on the system. (and *don't* use -O0 for production work!) Mark On Thu, Aug 20, 2015 at 9:05 PM Carlos Aguni sorla...@gmail.com wrote: Hello Mark! Thank you for your advice! I'm now using Gromacs-5.1. I've added -DGMX_BUILD_MDRUN_ONLY=ON on the previous cmake configuration. Here's my cmake and error log now: export TPREFIX=/home/ibm/softwares/gromacs/xlc/vsx/omp1/flagO0/ export flags1=-qnoinline -O0 -qsmp=omp export blaslapackflags=-L/usr/lib -lessl -L/opt/ibm/xlf/15.1.2/lib/ -lxlf90 -lxlf90_t -L/opt/ibm/xlsmp/4.1.2/lib -lxlomp_ser cmake .. -DGMX_MPI=on -DGMX_DOUBLE=off -DCMAKE_INSTALL_PREFIX=$TPREFIX -DBUILD_SHARED_LIBS=OFF -DGMX_FFT_LIBRARY=essl -DGMX_OPENMP=on -DCMAKE_VERBOSE_MAKEFILE=on -DGMX_GPU=off -DGMX_EXTERNAL_LAPACK=ON -DGMX_EXTERNAL_BLAS=ON -DGMX_BLAS_USER=$blaslapackflags -DGMX_LAPACK_USER=$blaslapackflags -DCMAKE_CXX_FLAGS=$flags1 -DCMAKE_C_FLAGS=$flags1 -DGMX_THREAD_MPI=off -DGMX_SIMD=IBM_VSX -DCMAKE_C_COMPILER=mpixlc -DCMAKE_CXX_COMPILER=mpixlc++ -DFFT_LINKER_FLAGS= -DLINEAR_ALGEBRA_LIBRARIES= -DCOVERAGE_EXTRA_FLAGS= -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_SHARED_LINKER_FLAGS=-qnoextname -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BUILD_SHARED_EXE=OFF - Error log: Linking CXX executable ../../bin/mdrun_mpi cd /home/ibm/crash/2gromacs-5.1-agosto/gromacs-5.1/single/src/programs /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun.dir/link.txt --verbose=1 /usr/bin/mpixlc++-qarch=auto -qaltivec -std=c++0x -qnoinline -O0 -qsmp=omp -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -O3 -DNDEBUG CMakeFiles/mdrun.dir/mdrun_main.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/membed.c.o CMakeFiles/mdrun_objlib.dir/mdrun/resource-division.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/runner.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/md.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/repl_ex.cpp.o -o ../../bin/mdrun_mpi -rdynamic ../../lib/libgromacs_mdrun_mpi.a -lrt /opt/ibmmath/essl/5.3/FFTW3/src/lib64/libfftw3_essl.a -L/usr/lib -lessl -L/opt/ibm/xlf/15.1.2/lib/ -lxlf90 -lxlf90_t -L/opt/ibm/xlsmp/4.1.2/lib -lxlomp_ser ../../lib/libgromacs_mdrun_mpi.a(copyrite.cpp.o): In function `gmx_print_version_info(_IO_FILE*)': copyrite.cpp:(.text+0x1310): undefined reference to `gmx_fft_get_version_info' copyrite.cpp:(.text+0x15f4): undefined reference to `gmx_fft_get_version_info' ../../lib/libgromacs_mdrun_mpi.a(fft.cpp.o): In function `gmx_fft_init_many_1d': fft.cpp:(.text+0x98): undefined reference to `gmx_fft_init_1d' ../../lib/libgromacs_mdrun_mpi.a(fft.cpp.o): In function `gmx_fft_init_many_1d_real': fft.cpp:(.text+0x1a8): undefined reference to `gmx_fft_init_1d_real' ../../lib/libgromacs_mdrun_mpi.a(fft.cpp.o): In function `gmx_many_fft_destroy': fft.cpp:(.text+0x300): undefined reference to `gmx_fft_destroy' ../../lib/libgromacs_mdrun_mpi.a(fft.cpp.o): In function `gmx_fft_many_1d_real$AF7_4': fft.cpp:(.text+0xfd0): undefined reference to `gmx_fft_1d_real' ../../lib/libgromacs_mdrun_mpi.a(fft.cpp.o): In function `gmx_fft_many_1d$AF8_3': fft.cpp:(.text+0x10c0): undefined reference to `gmx_fft_1d' Thanks in advance! Carlos. On Thu, Aug 20, 2015 at 7:42 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, GROMACS 5.1 is out, please don't install 5.1-rc1 any more. There's a little bit of advice about using custom linear algebra libraries at http://manual.gromacs.org/documentation/5.1/install-guide/index.html#linear-algebra-libraries but you don't need to bother with such libraries unless you know mdrun will be used to do normal-mode analysis or something. You might still run into problems - if so, we'll want to know how you ran cmake in the first place. Mark On Thu, Aug 20, 2015 at 1:20 AM Carlos Aguni sorla...@gmail.com wrote: Helo guys! I'm trying to compile Gromacs-5.1-rc1 with XLC 13.1.2 ESSL 5.3 and I'm facing an undefined reference error. Here's what I got: $ cd /home/ibm/crash/gromacs-agosto/2/gromacs-5.1-rc1/single/share/template /usr/bin/cmake -E cmake_link_script CMakeFiles/template.dir/link.txt --verbose=1 $ /usr/bin/mpixlc++-qarch=auto -qaltivec -std=c++0x -qnoinline -O0 -qsmp=omp -Wextra -Wno-missing-field-initializers -Wpointer-arith
Re: [gmx-users] What's the point of adding ions to neutralize the system?
You said it yourself: to neutralize the net charge of the system. Victor 2015-08-20 14:58 GMT-05:00 Jorge Fernandez de Cossio Diaz cos...@cim.sld.cu : Since the ion added is usually very far away from the protein (or molecule of interest), I don't see how it can affect the results of the molecular dynamics simulation. So why is it so important to add ions to neutralize the net-charge of the system? --- [http://5.cim.co.cu/cim.gif] -- 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] Broken protein chain: WARNING: Listed nonbonded interaction between particles ...
On 8/20/15 4:29 PM, Jorge Fernandez de Cossio Diaz wrote: Tried using -merge interactive -chainsep id on pdb2gmx, but I still get the same WARNING: WARNING: Listed nonbonded interaction between particles 2897 and 2908 at distance 3f which is larger than the table limit 3f nm. The energy minimization step prints this as a warning and proceeds, but when I try to equilibrate the system later, the warning becomes an error and it doesn't let me proceed, so this seems to be important. Also, it doesn't make sense to me that 2897 and 2908 are interacting, because even though they are consecutive (because of missing residues), they are very far apart in space. So why is it that when I put the fragments into the same chain, the topology creates this spurious interaction? Because you're ignoring something physically relevant - you have missing residues! pdb2gmx certainly gave long bond warnings when you produced the topology. You need to model in the missing residues, otherwise the structure is useless to you. -Justin -- Message: 4 Date: Thu, 20 Aug 2015 19:00:29 + From: Mark Abraham mark.j.abra...@gmail.com To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded interaction between particles ... Message-ID: CAMNuMARXoFeT_HN0J57y2pt=gzatnzgb+11asgpm6dxvyq3...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Hi, Yes, see pdbgmx -h about merge. Probably you want -merge interactive -chainsep id Mark On Thu, Aug 20, 2015 at 8:39 PM Jorge Fernandez de Cossio Diaz cos...@cim.sld.cu wrote: Hi all, I have a PDB file containing two proteins. One of the proteins has a long stretch of missing residues. When I try to energy-minimize it, I get the following: WARNING: Listed nonbonded interaction between particles 2897 and 2908 at distance 3f which is larger than the table limit 3f nm. Now, it turns out that atoms 2897 and 2908 belong to the residues between which the missing sequence lies. They are very far apart (because the missing stretch is quite long), so I don't think there should be any interaction between them. However, this WARNING seems to be saying that for some reason, the topology generated included an interaction between them, probably because it interpreted that since the two residues are consecutive in the PDB file, they are bonded (which they aren't, because of the missing residues). After trying some things, I realized that if I remove the option -chainsep id from pdb2gmx when I generate the topology, I don't get this warning. Instead, I get a bunch of topology files, each corresponding to a fragment of each chain, instead of a topology per chain. This is very hard to deal with, because, for example, if I want to make a position restrain on the backbone of each chain, I have to keep track of each fragment separately. Is there a way to fix the WARNING above without having to remove the option -chainsep id from pdb2gmx? Thanks. Best, cossio --- --- [http://5.cim.co.cu/cim.gif] -- == 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] simulations of ice beginning to spin
Hello, I'm sorry to submit a query twice, but I have not received a reply since last week. The original message is below. As the subject line states, my simulations are developing a rotation that I cannot explain. I was wondering if the box size could be an issue, so I redid both simulations in NPT with the Parrinello-Rahman Barostat. It did not solve the rotation problem. Both outputs looked very similar to the results from NVT. In addition, the corners of the cubic simulation still became disordered. That's the only update I have. Please see below for further details. Thanks! Regards, Nathan - Original Message - From: Nathan K Houtz nho...@purdue.edu To: gromacs org gmx-users gromacs.org_gmx-users@maillist.sys.kth.se Sent: Thursday, August 13, 2015 10:57:43 PM Subject: simulations of ice beginning to spin Hello, I am simulating two kinds of ice: ice Ih and ice Ic (cubic ice). Both simulations seem to have developed some rotation spontaneously and I'd like to know if I can control that somehow. I'm also simulating one in a triclinic box but the output gro file appears cubic. I'm not sure if I should be concerned about that or not. Lastly, the Ice Ic structure begins to fall apart during my simulation and I don't think it should. I'd appreciate help on any of these matters. Here are some more details: Ice Ih is done in a triclinic box, and originally looks like this: http://imgur.com/VQg9xQz. I use a rigid TIP4P/Ice water model, constrained by shake, and simulate it in NVT for 1,000,000 time steps (2 ns) at a temperature of 217K and a density of 0.920 g/cm3. At the end, it looks like this: http://imgur.com/8uzddRH. First of all, I'm wondering if gromacs has correctly applied the triclinic box, as it appears that periodic boundary conditions have turned it into a cube. VMD is showing the box described by the .gro file. Secondly, it has been rotated, at least a few degrees, about the z axis. It did not noticeably rotate about the x or y axes. I'm not sure how to explain how the simulation would develop any angular momentum. In my .mdp file, I have gromacs get rid of angular momentum every 100 steps, but I don't think it should develop any in the first place. Any advice? The other simulation, ice ic, didn't go quite as well. Here is the original orientation, viewed from one of the corners: http://imgur.com/i0ncpju (I realize the orthographic projections make it harder to see the actual structure, but they make it easier to see unique patterns from various angles, which I'm trying to use to determine how it has rotated). This one was also simulated for 1,000,000 timesteps (2 ns) at 217K with TIP4P/Ice constrained by shake, but at a density of 0.931 g/cm3. The resulting structure is this: http://imgur.com/Lwl8UUw. I'm not sure I've got the exact corresponding orientation in this view here, but I believe it is. It's looking down the x-axis this time. This simulation got rotated much worse. Here are the before and after views looking down the z-axis, just like I showed for the ice Ih above: http://imgur.com/a/LRQR3. With such a large number of timesteps, I cannot output enough frames in the trajectory file to view this as a smooth movie and ide ntify exactly when and why these rotations happen. It's more like a very long and rapid slide show. For the ice Ic, at least, it is possible that the whole box did not rotate, but all of the molecules simply reoriented themselves. But since at least part of the box appears to still be in the ice Ic structure, I'm not sure why they would do that. Ice Ic is only metastable at any temperature, so I would assume that if it falls apart, the structure would not come back. This is another issue. I would like to still have cubic ice structure at the end of this simulation, but clearly two of the corners have disastrously broken up. However, what looks like most of the molecules appear to still retain the structure. Do you think that it could be a problem with my box size, or the orientation? I'd like to know what things I might try to prevent the disintegration of the cubic structure. Thanks for any help. Regards, Nathan -- 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] Broken protein chain: WARNING: Listed nonbonded
On 8/20/15 5:21 PM, Jorge Fernandez de Cossio Diaz wrote: Note that I am adding position restrains to fix all the termini of the incomplete fragments. Shouldn't that take care of the missing residues? If there's a bond between residues that are separated by a large gap, the magnitude of the bonded force is going to be orders of magnitude larger than any restraint force. You need to fix your missing residues. No amount of hacking or trickery is going to give you a sensible result here. -Justin -- Message: 5 Date: Thu, 20 Aug 2015 20:29:42 + From: Jorge Fernandez de Cossio Diaz cos...@cim.sld.cu To: gromacs.org_gmx-users@maillist.sys.kth.se gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded interaction between particles ... Message-ID: fcd5150195922740996c04d9f8a6dfbb52c4c...@cimex2010mb1.cim.sld.cu Content-Type: text/plain; charset=us-ascii Tried using -merge interactive -chainsep id on pdb2gmx, but I still get the same WARNING: WARNING: Listed nonbonded interaction between particles 2897 and 2908 at distance 3f which is larger than the table limit 3f nm. The energy minimization step prints this as a warning and proceeds, but when I try to equilibrate the system later, the warning becomes an error and it doesn't let me proceed, so this seems to be important. Also, it doesn't make sense to me that 2897 and 2908 are interacting, because even though they are consecutive (because of missing residues), they are very far apart in space. So why is it that when I put the fragments into the same chain, the topology creates this spurious interaction? -- Message: 4 Date: Thu, 20 Aug 2015 19:00:29 + From: Mark Abraham mark.j.abra...@gmail.com To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded interaction between particles ... Message-ID: CAMNuMARXoFeT_HN0J57y2pt=gzatnzgb+11asgpm6dxvyq3...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Hi, Yes, see pdbgmx -h about merge. Probably you want -merge interactive -chainsep id Mark On Thu, Aug 20, 2015 at 8:39 PM Jorge Fernandez de Cossio Diaz cos...@cim.sld.cu wrote: Hi all, I have a PDB file containing two proteins. One of the proteins has a long stretch of missing residues. When I try to energy-minimize it, I get the following: WARNING: Listed nonbonded interaction between particles 2897 and 2908 at distance 3f which is larger than the table limit 3f nm. Now, it turns out that atoms 2897 and 2908 belong to the residues between which the missing sequence lies. They are very far apart (because the missing stretch is quite long), so I don't think there should be any interaction between them. However, this WARNING seems to be saying that for some reason, the topology generated included an interaction between them, probably because it interpreted that since the two residues are consecutive in the PDB file, they are bonded (which they aren't, because of the missing residues). After trying some things, I realized that if I remove the option -chainsep id from pdb2gmx when I generate the topology, I don't get this warning. Instead, I get a bunch of topology files, each corresponding to a fragment of each chain, instead of a topology per chain. This is very hard to deal with, because, for example, if I want to make a position restrain on the backbone of each chain, I have to keep track of each fragment separately. Is there a way to fix the WARNING above without having to remove the option -chainsep id from pdb2gmx? Thanks. Best, cossio --- --- [http://5.cim.co.cu/cim.gif] -- Message: 6 Date: Thu, 20 Aug 2015 16:40:27 -0400 From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded interaction between particles ... Message-ID: 55d63b3b.6040...@vt.edu Content-Type: text/plain; charset=windows-1252; format=flowed On 8/20/15 4:29 PM, Jorge Fernandez de Cossio Diaz wrote: Tried using -merge interactive -chainsep id on pdb2gmx, but I still get the same WARNING: WARNING: Listed nonbonded interaction between particles 2897 and 2908 at distance 3f which is larger than the table limit 3f nm. The energy minimization step prints this as a warning and proceeds, but when I try to equilibrate the system later, the warning becomes an error and it doesn't let me proceed, so this seems to be important. Also, it doesn't make sense to me that 2897 and 2908 are interacting, because even though they are consecutive (because of missing residues), they are very far apart in space. So why is it that when I put the fragments
Re: [gmx-users] Non Periodic Coordinate File
On 8/20/15 5:59 PM, ANAND AMITKUMAR Dharia wrote: Hello, I was wondering if it was possible to create a non-periodic coordinate file using trjconv or some other gromacs program on a trajectory file. I would like to use coordinate data to calculate displacement in order to compute a crosscorrelation between molecules, however, with the jumps in the coordinate file, there is no meaningful result. I understand I can use the -ur pbc mol command, but this just makes the molecule whole before bouncing across the screen. Any input would be helpful. trjconv -pbc nojump -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] simulations of ice beginning to spin
Hello Nathan, Did you set comm-mode and nstcomm http://manual.gromacs.org/online/mdp_opt.html#run in your mdp file? Best, Eric On Thu, Aug 20, 2015 at 3:37 PM, Nathan K Houtz nho...@purdue.edu wrote: Hello, I'm sorry to submit a query twice, but I have not received a reply since last week. The original message is below. As the subject line states, my simulations are developing a rotation that I cannot explain. I was wondering if the box size could be an issue, so I redid both simulations in NPT with the Parrinello-Rahman Barostat. It did not solve the rotation problem. Both outputs looked very similar to the results from NVT. In addition, the corners of the cubic simulation still became disordered. That's the only update I have. Please see below for further details. Thanks! Regards, Nathan - Original Message - From: Nathan K Houtz nho...@purdue.edu To: gromacs org gmx-users gromacs.org_gmx-users@maillist.sys.kth.se Sent: Thursday, August 13, 2015 10:57:43 PM Subject: simulations of ice beginning to spin Hello, I am simulating two kinds of ice: ice Ih and ice Ic (cubic ice). Both simulations seem to have developed some rotation spontaneously and I'd like to know if I can control that somehow. I'm also simulating one in a triclinic box but the output gro file appears cubic. I'm not sure if I should be concerned about that or not. Lastly, the Ice Ic structure begins to fall apart during my simulation and I don't think it should. I'd appreciate help on any of these matters. Here are some more details: Ice Ih is done in a triclinic box, and originally looks like this: http://imgur.com/VQg9xQz. I use a rigid TIP4P/Ice water model, constrained by shake, and simulate it in NVT for 1,000,000 time steps (2 ns) at a temperature of 217K and a density of 0.920 g/cm3. At the end, it looks like this: http://imgur.com/8uzddRH. First of all, I'm wondering if gromacs has correctly applied the triclinic box, as it appears that periodic boundary conditions have turned it into a cube. VMD is showing the box described by the .gro file. Secondly, it has been rotated, at least a few degrees, about the z axis. It did not noticeably rotate about the x or y axes. I'm not sure how to explain how the simulation would develop any angular momentum. In my .mdp file, I have gromacs get rid of angular momentum every 100 steps, but I don't think it should develop any in the first place. Any advice? The other simulation, ice ic, didn't go quite as well. Here is the original orientation, viewed from one of the corners: http://imgur.com/i0ncpju (I realize the orthographic projections make it harder to see the actual structure, but they make it easier to see unique patterns from various angles, which I'm trying to use to determine how it has rotated). This one was also simulated for 1,000,000 timesteps (2 ns) at 217K with TIP4P/Ice constrained by shake, but at a density of 0.931 g/cm3. The resulting structure is this: http://imgur.com/Lwl8UUw. I'm not sure I've got the exact corresponding orientation in this view here, but I believe it is. It's looking down the x-axis this time. This simulation got rotated much worse. Here are the before and after views looking down the z-axis, just like I showed for the ice Ih above: http://imgur.com/a/LRQR3. With such a large number of timesteps, I cannot output enough frames in the trajectory file to view this as a smooth movie and ide ntify exactly when and why these rotations happen. It's more like a very long and rapid slide show. For the ice Ic, at least, it is possible that the whole box did not rotate, but all of the molecules simply reoriented themselves. But since at least part of the box appears to still be in the ice Ic structure, I'm not sure why they would do that. Ice Ic is only metastable at any temperature, so I would assume that if it falls apart, the structure would not come back. This is another issue. I would like to still have cubic ice structure at the end of this simulation, but clearly two of the corners have disastrously broken up. However, what looks like most of the molecules appear to still retain the structure. Do you think that it could be a problem with my box size, or the orientation? I'd like to know what things I might try to prevent the disintegration of the cubic structure. Thanks for any help. Regards, Nathan -- 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
[gmx-users] Non Periodic Coordinate File
Hello, I was wondering if it was possible to create a non-periodic coordinate file using trjconv or some other gromacs program on a trajectory file. I would like to use coordinate data to calculate displacement in order to compute a crosscorrelation between molecules, however, with the jumps in the coordinate file, there is no meaningful result. I understand I can use the -ur pbc mol command, but this just makes the molecule whole before bouncing across the screen. Any input would be helpful. Thanks, Anand -- 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] Non Periodic Coordinate File
Wow, thank you so much, don't know how I didn't realize this. On Thu, Aug 20, 2015 at 3:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/20/15 5:59 PM, ANAND AMITKUMAR Dharia wrote: Hello, I was wondering if it was possible to create a non-periodic coordinate file using trjconv or some other gromacs program on a trajectory file. I would like to use coordinate data to calculate displacement in order to compute a crosscorrelation between molecules, however, with the jumps in the coordinate file, there is no meaningful result. I understand I can use the -ur pbc mol command, but this just makes the molecule whole before bouncing across the screen. Any input would be helpful. trjconv -pbc nojump -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] Incorrect number of parameters - found 3, expected 1 or 1 for Polarization.
Thank you professor Justin! I solved this error which comes from the decimals of the box dimensions. Initially, my box dimensions are 4.5*4.5*16 nm3 and the local pressure calculation does not work, but after I change them to be integers 4*4*16 nm3 in the gro file, the simulation works. It is strange for me. I do not know why. Best wishes, Xiaohui Date: Thu, 20 Aug 2015 16:44:58 -0400 From: jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Incorrect number of parameters - found 3, expected 1 or 1 for Polarization. On 8/20/15 4:01 PM, 折晓会 wrote: Thank you professor Justin! I solved this error with your suggestion. When I use mdrun -rerun to calculate the local pressure, another error occurs: Fatal error: Rerun trajectory frame step 60 time 600.00 has too small box dimensions What does this mean? It means your box is too small. What are the box dimensions in that frame, and what are the cutoffs you are using? -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] Problem compiling Gromacs 5.1
Just use your favourite text editor.
Peter
On Thu, Aug 20, 2015 at 3:10 AM, atsutoshi0...@gmail.com wrote:
Line 52 of cmake/FindSphinx.cmake file is written below.
string(REGEX REPLACE Sphinx \\([^)]*\\) ([^ ]+) \\1
SPHINX_EXECUTABLE_VERSION ${SPHINX_VERSION_OUTPUT_VARIABLE})
Can you tell me how I can change the line?
Bests,
Leucer
2015/08/19 23:11、Mark Abraham mark.j.abra...@gmail.com のメッセージ:
Hi,
On Wed, Aug 19, 2015 at 3:49 PM 岡部篤俊 atsutoshi0...@gmail.com wrote:
Hi,
I am unable to compile Gromamcs 5.1 using the following cmake command.
cmake .. -DGMX_FFT_LIBRARY=fftpack
-DCMAKE_INSTALL_PREFIX=gromacs/gromacs-5.1 -DGMX_DOUBLE=off
-DGMX_THREAD_MPI=off -DGMX_MPI=on -DGMX_CPU_ACCELERATION=SSE4.1
Unrelated, but you now need to use -DGMX_SIMD=SSE4.1 to have the same
effect.
-DGMX_USE_RDTSCP=off
Then I got the error message.
Boost = 1.44 not found. Using minimal internal version. This may cause
trouble if you plan on compiling/linking other software that uses Boost
against GROMACS.
CMake Error at cmake/FindSphinx.cmake:52 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments total
to
command.
Call Stack (most recent call first):
docs/CMakeLists.txt:62 (find_package)
Could you advice what could be causing this error?
We try to find Sphinx in case people want to build the new documentation,
but it looks like some part of the detection isn't reliable enough. Can
you
please try changing line 52 of cmake/FindSphinx.cmake to read
string(REGEX REPLACE Sphinx \\([^)]*\\) ([^ ]+) \\1
SPHINX_EXECUTABLE_VERSION ${SPHINX_VERSION_OUTPUT_VARIABLE})
and let us know how you go?
Mark
I was able to compile Gromacs 5.0 using same cmake command….
Bests,
Leucer
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[gmx-users] Adding HSD residue to AMBER ff99SB-ILDN
Hi everyone, I have a .pdb file of the WW domain of human FIP35 protein extracted from an MD calculation obtained with AMBER ff99SB-ILDN and solvent type tip3. Now I need to obtain the topology out of it, but the .pdb contains a residue, namely HSD, which is not present in the Amber residue database. I looked at the source files and found out that CHARMM has it. In particular, this is what you can find in the CHARMM database: [ HSD ] [ atoms ] N NH1 -0.47 0 HN H 0.31 1 CA CT1 0.07 2 HA HB 0.09 3 CB CT2 -0.09 4 HB1 HA 0.09 5 HB2 HA 0.09 6 ND1 NR1 -0.36 7 HD1 H 0.32 8 CG CPH1 -0.05 9 CE1 CPH2 0.25 10 HE1 HR1 0.13 11 NE2 NR2 -0.70 12 CD2 CPH1 0.22 13 HD2 HR3 0.10 14 C C 0.51 15 O O -0.51 16 [ bonds ] CB CA CG CB ND1 CG CE1 ND1 NE2 CD2 N HN N CA C CA C +N CA HA CB HB1 CB HB2 ND1 HD1 CD2 HD2 CE1 HE1 O C CG CD2 CE1 NE2 [ impropers ] ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 ND1 CE1 CG HD1 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 N -C CA HN C CA +N O [ cmap ] -C N CA C +N Is there any possible way in which I can copy and paste this in the Amber database and hope it will work correctly? Thank you very much!!! -- 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] High load imbalance: 31.8%
On Thu, Aug 20, 2015 at 5:52 PM, Szilárd Páll pall.szil...@gmail.com wrote: Hi, You're not pinning threads and it seems that you're running on a large SMP machine! Assuming that the 512 threads reported (line 91) is correct that's a 32 socket SMP machine, perhaps an SGI UV? In any case Xeon E5-4xxx is typically deployed in 4-8 socket installations, Correction: I confused the E5-46xx with the E7 series. These are 2-4 socket, it seems. In any case, the 512 threads reported still suggests a large SMP machine. so your 8 threads will be floating around on a number of CPUs which ruins your performance - and likely contributes to the varying and large load imbalance. My advice: - don't ignore notes/warnings issued by mdrun (line 366, should be on the standard out too), we put quite some though into spamming users only when relevant :) - pin mdrun and/or its threads either with -pin on (and -pinoffset if needed) or with whatever tools your admins provide/recommend [Extras: consider using FFTW even with the Intel compilers it's often faster for our small FFTs than MKL; and GNU iso Intel compiler is often faster too.] Fixing the above issues should not only reduce imbalance but most likely also allow you to gain quite some simulation performance! Let us know if it worked. Cheers, -- Szilárd On Thu, Aug 20, 2015 at 5:08 PM, Nash, Anthony a.n...@ucl.ac.uk wrote: Hi Mark, Many thanks for looking into this. One of the log files (the job hasn’t finished running) is here: https://www.dropbox.com/s/zwrro54yni2uxtn/umb_3_umb.log?dl=0 The system is a soluble collagenase in water with a collagen substrate and two zinc co-factors. There are 287562 atoms in the system. Please let me know if you need to know anything else. Thanks! Anthony On 20/08/2015 11:39, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, In cases like this, it's good to describe what's in your simulation, and share the full .log file on a file-sharing service, so we can see both the things mdrun reports early and late. Mark On Thu, Aug 20, 2015 at 8:22 AM Nash, Anthony a.n...@ucl.ac.uk wrote: Hi all, I appear to have a very high load imbalance on some of my runs. Values starting from approx. 7% up to 31.8% with reported vol min/aver of around 0.6 (I haven¹t found one under half yet). When I look through the .log file at the start of the run I see: Initializing Domain Decomposition on 8 ranks Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 0.514 nm, LJ-14, atoms 3116 3123 multi-body bonded interactions: 0.429 nm, Proper Dih., atoms 3116 3123 Minimum cell size due to bonded interactions: 0.472 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.862 nm Estimated maximum distance required for P-LINCS: 0.862 nm This distance will limit the DD cell size, you can override this with -rcon Using 0 separate PME ranks, as there are too few total ranks for efficient splitting Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 8 cells with a minimum initial size of 1.077 nm The maximum allowed number of cells is: X 12 Y 12 Z 12 Domain decomposition grid 4 x 2 x 1, separate PME ranks 0 PME domain decomposition: 4 x 2 x 1 Domain decomposition rank 0, coordinates 0 0 0 Using 8 MPI processes Using 1 OpenMP thread per MPI process Having a quick look through the documentation and I see that I should consider implementing the verlet cut-off (which I am) and adjust the number of PME nodes/cut-off and PME grid spacing. Would this simply be a case of throwing more cores at the simulation or must I play around with P-LINCS parameters? Thanks Anthony -- 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] Fatal error: Index contains atom numbers larger than the topology
Hi! I am running a DoS calculation using g_dos on 5.0.6 version, using the .tpr used to generate a .trr trajectory. Hence, the topology and index should contain the same number of atoms and I confirmed this by looking the number of atoms on the generated .gro. Still, I got the error: Command = *g_dos_506 -s ani.DOS.tpr -f ani.DOS.trr -beginfit 20 -endfit 40 -T 298 -dos ani.dos.xvg* *Reading file ani.DOS.tpr, VERSION 5.0.6 (single precision)Reading file ani.DOS.tpr, VERSION 5.0.6 (single precision)Group 0 ( System) has 14000 elementsGroup 1 ( Other) has 14000 elementsGroup 2 (ANI) has 14000 elementsSelect a group: 0---Program g_dos_506, VERSION 5.0.6Fatal error:Index contains atom numbers larger than the topology* Does anyone have an idea about it? Cheers! -- Marcelo Depólo Polêto Group of Structural Bioinformatics - Center of Biotechnology Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- 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] High load imbalance: 31.8%
Hi Szilárd Thanks for all of that advice. I’m going to have to take a lot of this up with the Cluster Service Staff. This is a new cluster service I won a grant for, thus not my usual platform which would typically yield an imbalance of somewhere around 0.8% to 2%. Thanks again Anthony On 20/08/2015 16:52, Szilárd Páll pall.szil...@gmail.com wrote: Hi, You're not pinning threads and it seems that you're running on a large SMP machine! Assuming that the 512 threads reported (line 91) is correct that's a 32 socket SMP machine, perhaps an SGI UV? In any case Xeon E5-4xxx is typically deployed in 4-8 socket installations, so your 8 threads will be floating around on a number of CPUs which ruins your performance - and likely contributes to the varying and large load imbalance. My advice: - don't ignore notes/warnings issued by mdrun (line 366, should be on the standard out too), we put quite some though into spamming users only when relevant :) - pin mdrun and/or its threads either with -pin on (and -pinoffset if needed) or with whatever tools your admins provide/recommend [Extras: consider using FFTW even with the Intel compilers it's often faster for our small FFTs than MKL; and GNU iso Intel compiler is often faster too.] Fixing the above issues should not only reduce imbalance but most likely also allow you to gain quite some simulation performance! Let us know if it worked. Cheers, -- Szilárd On Thu, Aug 20, 2015 at 5:08 PM, Nash, Anthony a.n...@ucl.ac.uk wrote: Hi Mark, Many thanks for looking into this. One of the log files (the job hasn’t finished running) is here: https://www.dropbox.com/s/zwrro54yni2uxtn/umb_3_umb.log?dl=0 The system is a soluble collagenase in water with a collagen substrate and two zinc co-factors. There are 287562 atoms in the system. Please let me know if you need to know anything else. Thanks! Anthony On 20/08/2015 11:39, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, In cases like this, it's good to describe what's in your simulation, and share the full .log file on a file-sharing service, so we can see both the things mdrun reports early and late. Mark On Thu, Aug 20, 2015 at 8:22 AM Nash, Anthony a.n...@ucl.ac.uk wrote: Hi all, I appear to have a very high load imbalance on some of my runs. Values starting from approx. 7% up to 31.8% with reported vol min/aver of around 0.6 (I haven¹t found one under half yet). When I look through the .log file at the start of the run I see: Initializing Domain Decomposition on 8 ranks Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 0.514 nm, LJ-14, atoms 3116 3123 multi-body bonded interactions: 0.429 nm, Proper Dih., atoms 3116 3123 Minimum cell size due to bonded interactions: 0.472 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.862 nm Estimated maximum distance required for P-LINCS: 0.862 nm This distance will limit the DD cell size, you can override this with -rcon Using 0 separate PME ranks, as there are too few total ranks for efficient splitting Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 8 cells with a minimum initial size of 1.077 nm The maximum allowed number of cells is: X 12 Y 12 Z 12 Domain decomposition grid 4 x 2 x 1, separate PME ranks 0 PME domain decomposition: 4 x 2 x 1 Domain decomposition rank 0, coordinates 0 0 0 Using 8 MPI processes Using 1 OpenMP thread per MPI process Having a quick look through the documentation and I see that I should consider implementing the verlet cut-off (which I am) and adjust the number of PME nodes/cut-off and PME grid spacing. Would this simply be a case of throwing more cores at the simulation or must I play around with P-LINCS parameters? Thanks Anthony -- 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
Re: [gmx-users] Fatal error: Index contains atom numbers larger than the topology
On 8/20/15 12:12 PM, Marcelo Depólo wrote: Hi! I am running a DoS calculation using g_dos on 5.0.6 version, using the .tpr used to generate a .trr trajectory. Hence, the topology and index should contain the same number of atoms and I confirmed this by looking the number of atoms on the generated .gro. This check tells you nothing of use. A .gro will always have the whole system in it; there's no way to write out a subset of atoms here via mdrun. Still, I got the error: Command = *g_dos_506 -s ani.DOS.tpr -f ani.DOS.trr -beginfit 20 -endfit 40 -T 298 -dos ani.dos.xvg* *Reading file ani.DOS.tpr, VERSION 5.0.6 (single precision)Reading file ani.DOS.tpr, VERSION 5.0.6 (single precision)Group 0 ( System) has 14000 elementsGroup 1 ( Other) has 14000 elementsGroup 2 (ANI) has 14000 elementsSelect a group: 0---Program g_dos_506, VERSION 5.0.6Fatal error:Index contains atom numbers larger than the topology* Does anyone have an idea about it? What does gmxcheck tell you about all the files involved? How did you generate the index file? As the error says, the problem comes from the index file specifying something that doesn't exist in the topology. -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.
