[gmx-users] Fwd: installing Gromacs4.6.3 on cygwin
Dear all I am installing gromacs -4.6.3 on cygwin with following commands tar -xvzf gramcs-4.6.3.tar.gz cd gromacs-4.6.3 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_DOUBLE=on It runs fine and write file in build directory. when I run make command it gives following error. [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_permute.c.o [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_position.c.o [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_same.c.o [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_simple.c.o [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/symrec.c.o [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/centerofmass.c.o [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/displacement.c.o [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/indexutil.c.o [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/nbsearch.c.o [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/poscalc.c.o [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/position.c.o [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/trajana.c.o [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/statistics/gmx_statistics.c.o [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/statistics/histogram.c.o [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/errhandler.c.o [ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/tmpi_malloc.c.o [ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/atomic.c.o In file included from /cygdrive/c/packages/gromacs-4.6.3/src/gmxlib/thread_mpi/atomic.c:38:0: /cygdrive/c/packages/gromacs-4.6.3/src/gmxlib/thread_mpi/impl.h:504:20: error: field ‘timer_init’ has incomplete type struct timeval timer_init; ^ src/gmxlib/CMakeFiles/gmx.dir/build.make:3070: recipe for target `src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/atomic.c.o' failed make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/atomic.c.o] Error 1 CMakeFiles/Makefile2:1238: recipe for target `src/gmxlib/CMakeFiles/gmx.dir/all' failed make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 Makefile:146: recipe for target `all' failed make: *** [all] Error 2 Please help me to install this version of gromacs on cygwin Shahid -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Umbrella sampling simulations using make_edi with -restrain and -harmonic
Hi all, I can't seem to find the correct combination of EDI parameters impose a harmonically-constrained simulation along an eigenvector in GROMACS 4.6.2, and I'd like to confirm that the inputs I have are actually correct. Here is the make_edi command I used to generate the .edi file fed to mdrun: echo C-alpha System | make_edi -restrain -harmonic \ -f ../ca-evec.trr \ -eig ../ca-eval.xvg \ -s ../analysis.tpr \ -ori ./init.gro \ -outfrq 2500 -deltaF0 150 -Eflnull 100 -flood 1 \ -o constrain.edi Where the eigenvectors and eigenvalues are previously derived by g_covar for a set of unrestrained trajectories. The origin file init.gro is the same as the starting coordinates of this constrained run, extracted from a previous EDI run to start at an appropriate location on the eigenvector space. The 1st eigenvalue is ~ 66, and the eigenvector looked fine in VMD when plotted by g_anaeig -extr. So mdrun -ei constrain.edi runs normally, but the flooding potential drops to zero so the protein diffuses freely along the 1st eigenvector. e.g. the first/last line in edsam.xvg looks like: # time RMSD EV1projFLOOD EV1-Ef1 EV1-Vf1 EV1-deltaF 0.0 0.43 9.99 -9.4e+1 9.5e-8 3.8e-9 -5.3e-4 10.0 0.40 9.49 0.0 -0.0 1.6e-44-0.0 ... 1.00 0.94 -2.2 0.0 -0.0 1.6e-44-0.0 When c(0) is supposed to be according 9.99 as I set init.gro to be the -ori. Do I need to change -alpha as well? What parameters am I missing/added by mistake? The manual gives no indication as to which ones to do. = = = P.S. the relevant constrain.edi lines contain: ... #DELTA_F0 150.00 #INIT_DELTA_F 0.0 #TAU 0.10 #EFL_NULL -100.00 #ALPHA2 -1.0 #KT 2.50 #HARMONIC 1 #CONST_FORCE_FLOODING 0 ... -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella sampling simulations using make_edi with -restrain and -harmonic
Hi Po-chia, On Sep 10, 2013, at 9:53 AM, Chen, Po-chia pc...@gwdg.de wrote: Hi all, I can't seem to find the correct combination of EDI parameters impose a harmonically-constrained simulation along an eigenvector in GROMACS 4.6.2, and I'd like to confirm that the inputs I have are actually correct. Here is the make_edi command I used to generate the .edi file fed to mdrun: echo C-alpha System | make_edi -restrain -harmonic \ -f ../ca-evec.trr \ -eig ../ca-eval.xvg \ -s ../analysis.tpr \ -ori ./init.gro \ -outfrq 2500 -deltaF0 150 -Eflnull 100 -flood 1 \ -o constrain.edi I think you should add -tau 0 when using flooding as harmonic restraint (since you do not want the flooding potential to change). Where the eigenvectors and eigenvalues are previously derived by g_covar for a set of unrestrained trajectories. The origin file init.gro is the same as the starting coordinates of this constrained run, extracted from a previous EDI run to start at an appropriate location on the eigenvector space. The 1st eigenvalue is ~ 66, and the eigenvector looked fine in VMD when plotted by g_anaeig -extr. So mdrun -ei constrain.edi runs normally, but the flooding potential drops to zero so the protein diffuses freely along the 1st eigenvector. e.g. the first/last line in edsam.xvg looks like: # time RMSD EV1projFLOOD EV1-Ef1 EV1-Vf1 EV1-deltaF 0.0 0.43 9.99 -9.4e+1 9.5e-8 3.8e-9 -5.3e-4 10.0 0.40 9.49 0.0 -0.0 1.6e-44-0.0 ... 1.00 0.94 -2.2 0.0 -0.0 1.6e-44-0.0 When c(0) is supposed to be according 9.99 as I set init.gro to be the -ori. Do I need to change -alpha as well? What parameters am I missing/added by mistake? The manual gives no indication as to which ones to do. Can you check whether make_edi -ori wrote the correct position on the 1st eigenvector in your .edi file? Scroll down to a line called # NUMBER OF EIGENVECTORS + COMPONENTS GROUP 7 (Group 7 means the flooding vectors), if you have a single flooding vector, the next line should read 1 and in the following line you will find three entries that describe nr spring constant reference projection ref. proj. change per time step which I guess read in your case 1 19.99 no 4th entry so the reference projection should be 9.99, as calculated from your .ori structure. If there is no 3rd entry, you can simply put it there manually (and leave away the -ori option to make_edi). Best, Carsten = = = P.S. the relevant constrain.edi lines contain: ... #DELTA_F0 150.00 #INIT_DELTA_F 0.0 #TAU 0.10 #EFL_NULL -100.00 #ALPHA2 -1.0 #KT 2.50 #HARMONIC 1 #CONST_FORCE_FLOODING 0 ... -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Adding ligand structure information obtained from ATB into the pdb2gmx gro file (obtained using GROMACS)
Dear Users, I am using the ATB web server to build topologies of my ligands. I have tried to include the ligand UNITED ATOM STRUCTURE (generated by the ATB) into my protein gro file generated by GROMACS by copying the information in the lines starting with HETAM to the end of my protein gro file and updating the number of molecules at the beginning of the file so as to reflect the change. However, i am getting an error when i run the editconf command = Fatal error: Something is wrong in the coordinate formatting of file ../2oul_processed.gro. Note that gro is fixed format. My ligand link is = http://compbio.biosci.uq.edu.au/atb/download.py?session=14360 Can anyone tell me how to solve this. Thank you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] xpm2ps
Hi Gromacs mailing list supporters, I had previously posted query on xpm2ps. http://lists.gromacs.org/pipermail/gmx-users/2013-April/080729.html There are 100 frames in the simulations. I tried fiddling with the parameters in the .m2p file such as matrix spacing and X-axis minimum and maximum tick spacing however I always get black lines at the bottom instead of X-axis. Your input is appreciated. -- Regards, Dr. Neha S. Gandhi, Curtin Research Fellow, School of Biomedical Sciences, Curtin University, Perth GPO U1987 Australia LinkedIn Research Gate -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Adding ligand structure information obtained from ATB into the pdb2gmx gro file (obtained using GROMACS)
You cannot mix the .gro and .pdb formats within the same file. One approach is to direct the GROMACS tool to write the output in pdb format simply by naming the output file with a .pdb suffix. Then you can do such a pasting operation, and if you've preserved the format correctly, proceed to use the resulting file in future GROMACS stages. Mark On Tue, Sep 10, 2013 at 11:10 AM, MUSYOKA THOMMAS mutemibiochemis...@gmail.com wrote: Dear Users, I am using the ATB web server to build topologies of my ligands. I have tried to include the ligand UNITED ATOM STRUCTURE (generated by the ATB) into my protein gro file generated by GROMACS by copying the information in the lines starting with HETAM to the end of my protein gro file and updating the number of molecules at the beginning of the file so as to reflect the change. However, i am getting an error when i run the editconf command = Fatal error: Something is wrong in the coordinate formatting of file ../2oul_processed.gro. Note that gro is fixed format. My ligand link is = http://compbio.biosci.uq.edu.au/atb/download.py?session=14360 Can anyone tell me how to solve this. Thank you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] xpm2ps
On 9/10/13 5:30 AM, Neha Gandhi wrote: Hi Gromacs mailing list supporters, I had previously posted query on xpm2ps. http://lists.gromacs.org/pipermail/gmx-users/2013-April/080729.html There are 100 frames in the simulations. I tried fiddling with the parameters in the .m2p file such as matrix spacing and X-axis minimum and maximum tick spacing however I always get black lines at the bottom instead of X-axis. An image of what you're dealing with would be useful, as would the full contents of the .m2p file you're using. Without that, there's not much anyone can do to help, aside from generically saying to increase the value of xtick. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Adding ligand structure information obtained from ATB into the pdb2gmx gro file (obtained using GROMACS)
Thanks Mark, I am now set and rolling down. Cheers. On Tue, Sep 10, 2013 at 11:55 AM, Mark Abraham mark.j.abra...@gmail.comwrote: You cannot mix the .gro and .pdb formats within the same file. One approach is to direct the GROMACS tool to write the output in pdb format simply by naming the output file with a .pdb suffix. Then you can do such a pasting operation, and if you've preserved the format correctly, proceed to use the resulting file in future GROMACS stages. Mark On Tue, Sep 10, 2013 at 11:10 AM, MUSYOKA THOMMAS mutemibiochemis...@gmail.com wrote: Dear Users, I am using the ATB web server to build topologies of my ligands. I have tried to include the ligand UNITED ATOM STRUCTURE (generated by the ATB) into my protein gro file generated by GROMACS by copying the information in the lines starting with HETAM to the end of my protein gro file and updating the number of molecules at the beginning of the file so as to reflect the change. However, i am getting an error when i run the editconf command = Fatal error: Something is wrong in the coordinate formatting of file ../2oul_processed.gro. Note that gro is fixed format. My ligand link is = http://compbio.biosci.uq.edu.au/atb/download.py?session=14360 Can anyone tell me how to solve this. Thank you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- *MUSYOKA THOMMAS MUTEMI Mob nos **+27844846540** B.Sc Biochemistry (Kenyatta University),MSc Pharmaceutical Science (Nagasaki University)* *PhD Student-Bioinformatics (Rhodes University) *Skype ID- MUSYOKA THOMMAS MUTEMI Alternative email - thom...@sia.co.ke * Do all the good you can, By all the means you can, In all the ways you can, In all the places you can, At all the times you can, To all the people you can, As long as ever you can. - John Wesley. * -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fwd: [gmx-users] xpm2ps
On 9/10/13 6:43 AM, Neha Gandhi wrote: Hi Justin, I am sorry to forward the files to your id but gromacs mailing list wouldn't allow attachments. Regardless, please keep the discussion on the list. An .m2p file is small enough that it can be copied and pasted into an email. Everything else should be posted online such that you can provide a URL to download other files. The image simply appears stretched, so the solution is to increase the ratio of ybox/xbox, by decreasing xbox by a few orders of magnitude and/or increasing ybox. Keep in mind that if you have a million frames and even a few hundred residues along the y-axis, your x-axis is still 10^4 units larger! The current ratio established by xbox = 0.1 ; x-size of a matrix element ybox = 5; y-size of a matrix element is only 50, so you naturally see a very stretched and unintelligible plot. -Justin Many thanks, Neha -- Forwarded message -- From: Neha Gandhi n.gandh...@gmail.com Date: 10 September 2013 18:35 Subject: Re: [gmx-users] xpm2ps To: Discussion list for GROMACS users gmx-users@gromacs.org I am attaching the files for your reference. On 10 September 2013 17:57, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 5:30 AM, Neha Gandhi wrote: Hi Gromacs mailing list supporters, I had previously posted query on xpm2ps. http://lists.gromacs.org/pipermail/gmx-users/2013-April/080729.html There are 100 frames in the simulations. I tried fiddling with the parameters in the .m2p file such as matrix spacing and X-axis minimum and maximum tick spacing however I always get black lines at the bottom instead of X-axis. An image of what you're dealing with would be useful, as would the full contents of the .m2p file you're using. Without that, there's not much anyone can do to help, aside from generically saying to increase the value of xtick. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Regards, Dr. Neha S. Gandhi, Curtin Research Fellow, School of Biomedical Sciences, Curtin University, Perth GPO U1987 Australia LinkedIn Research Gate -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NMR restrained MD
Hi Justin, This is another type of error while running energy minimization: what to do for these type of errors. ERROR 218 [file topol.top, line 23487]: No default Ryckaert-Bell. types ERROR 219 [file topol.top, line 23499]: No default Ryckaert-Bell. types ERROR 220 [file topol.top, line 23500]: No default Ryckaert-Bell. types ERROR 221 [file topol.top, line 23501]: No default Ryckaert-Bell. types ERROR 222 [file topol.top, line 23502]: No default Ryckaert-Bell. types ERROR 223 [file topol.top, line 23503]: No default Ryckaert-Bell. types ERROR 224 [file topol.top, line 23515]: No default Ryckaert-Bell. types --Rama On Mon, Sep 9, 2013 at 5:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/9/13 6:11 PM, Rama Krishna Koppisetti wrote: Hi Justin, I included 1 DMPC molecule parameters in the file should I need to include 128 molecules parameters in the file .rtp. No. Residue definitions are used any time they are encountered in the coordinate file. There is no need for such redundancy at the force field level. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NMR restrained MD
On 9/10/13 9:21 AM, Rama Krishna Koppisetti wrote: Hi Justin, This is another type of error while running energy minimization: what to do for these type of errors. They're exactly the same as the dihedral error from before. You're using parameters that don't exist in the force field. -Justin ERROR 218 [file topol.top, line 23487]: No default Ryckaert-Bell. types ERROR 219 [file topol.top, line 23499]: No default Ryckaert-Bell. types ERROR 220 [file topol.top, line 23500]: No default Ryckaert-Bell. types ERROR 221 [file topol.top, line 23501]: No default Ryckaert-Bell. types ERROR 222 [file topol.top, line 23502]: No default Ryckaert-Bell. types ERROR 223 [file topol.top, line 23503]: No default Ryckaert-Bell. types ERROR 224 [file topol.top, line 23515]: No default Ryckaert-Bell. types --Rama On Mon, Sep 9, 2013 at 5:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/9/13 6:11 PM, Rama Krishna Koppisetti wrote: Hi Justin, I included 1 DMPC molecule parameters in the file should I need to include 128 molecules parameters in the file .rtp. No. Residue definitions are used any time they are encountered in the coordinate file. There is no need for such redundancy at the force field level. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NMR restrained MD
Hi Justin, It is which part in the force field. Exactly which file I have to look to overcome this errors. Thanks --Rama On Tue, Sep 10, 2013 at 8:25 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 9:21 AM, Rama Krishna Koppisetti wrote: Hi Justin, This is another type of error while running energy minimization: what to do for these type of errors. They're exactly the same as the dihedral error from before. You're using parameters that don't exist in the force field. -Justin ERROR 218 [file topol.top, line 23487]: No default Ryckaert-Bell. types ERROR 219 [file topol.top, line 23499]: No default Ryckaert-Bell. types ERROR 220 [file topol.top, line 23500]: No default Ryckaert-Bell. types ERROR 221 [file topol.top, line 23501]: No default Ryckaert-Bell. types ERROR 222 [file topol.top, line 23502]: No default Ryckaert-Bell. types ERROR 223 [file topol.top, line 23503]: No default Ryckaert-Bell. types ERROR 224 [file topol.top, line 23515]: No default Ryckaert-Bell. types --Rama On Mon, Sep 9, 2013 at 5:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/9/13 6:11 PM, Rama Krishna Koppisetti wrote: Hi Justin, I included 1 DMPC molecule parameters in the file should I need to include 128 molecules parameters in the file .rtp. No. Residue definitions are used any time they are encountered in the coordinate file. There is no need for such redundancy at the force field level. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NMR restrained MD
On 9/10/13 9:33 AM, Rama Krishna Koppisetti wrote: Hi Justin, It is which part in the force field. Exactly which file I have to look to overcome this errors. Go to the line number in the .top indicated in the error message and determine the atom types. This will tell you the sequence of atom types involved in the R-B dihedral that is missing. In theory, you would then add missing parameters to ffbonded.itp, if they exist. -Justin On Tue, Sep 10, 2013 at 8:25 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 9:21 AM, Rama Krishna Koppisetti wrote: Hi Justin, This is another type of error while running energy minimization: what to do for these type of errors. They're exactly the same as the dihedral error from before. You're using parameters that don't exist in the force field. -Justin ERROR 218 [file topol.top, line 23487]: No default Ryckaert-Bell. types ERROR 219 [file topol.top, line 23499]: No default Ryckaert-Bell. types ERROR 220 [file topol.top, line 23500]: No default Ryckaert-Bell. types ERROR 221 [file topol.top, line 23501]: No default Ryckaert-Bell. types ERROR 222 [file topol.top, line 23502]: No default Ryckaert-Bell. types ERROR 223 [file topol.top, line 23503]: No default Ryckaert-Bell. types ERROR 224 [file topol.top, line 23515]: No default Ryckaert-Bell. types --Rama On Mon, Sep 9, 2013 at 5:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/9/13 6:11 PM, Rama Krishna Koppisetti wrote: Hi Justin, I included 1 DMPC molecule parameters in the file should I need to include 128 molecules parameters in the file .rtp. No. Residue definitions are used any time they are encountered in the coordinate file. There is no need for such redundancy at the force field level. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Fwd: installing Gromacs4.6.3 on cygwin
On 10.09.2013 08:20, shahid nayeem wrote: I am installing gromacs -4.6.3 on cygwin with following commands tar -xvzf gramcs-4.6.3.tar.gz cd gromacs-4.6.3 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_DOUBLE=on It runs fine and write file in build directory. when I run make command it gives following error. ... /cygdrive/c/packages/gromacs-4.6.3/src/gmxlib/thread_mpi/impl.h:504:20: error: field ‘timer_init’ has incomplete type struct timeval timer_init; ^ src/gmxlib/CMakeFiles/gmx.dir/build.make:3070: recipe for target The Gromacs-file gmxlib/thread_mpi/impl.h is missing the correct #define for the unixish Cygwin pseudo-os. You can add it by inserting #define HAVE_SYS_TIME_H at the very top of the file gmxlib/thread_mpi/impl.h Then the package will probably compile and link, but mdrun's thread-mpi (tMPI) will not work on Cygwin (didn't work last time I tried). So you could do the following: 1) install the Gromacs package with normal compilation, and 2) build and install the openmpi-version of mdrun (mdrun_mpi). (1) cmake-options for package: ... -DGMX_GPU=OFF \ -DGMX_PREFER_STATIC_LIBS=ON \ ... make -j4 install (delete all files from the build path) (2) cmake options for mdrun_mpi ... -DGMX_GPU=OFF\ -DGMX_MPI=ON \ -DGMX_PREFER_STATIC_LIBS=ON \ ... make -j4 install-mdrun The openmpi-version (mdrun_mpi) runs reasonable on Cygwin/64 1.7.25, but not as fast as the native windows version (compiled with visual studio 10 or 12). The windows-compiled version of 4.6.3 is very robust and allows to link mdrun against CUDA 5.0 (but not 5.5(+VC12) for unknown reasons). Then, you'll have full gpu support under windows. Regards M. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NMR restrained MD
Adding parameters can be a little bit of a pain, you could instead change the atom types in the molecule parameter, to ones that have defined angles and bond types with each other. Of course, you would need to make sure that you dont assign sp2 with sp3 atoms, or aromatic with non aromatic etc. Check out ffbonded in the appropriate forcefield folder to see which atomtypes have defined bond types. Check out atomtypes.atp to see all the atom types for the forcefield On Tue, Sep 10, 2013 at 6:40 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 9:33 AM, Rama Krishna Koppisetti wrote: Hi Justin, It is which part in the force field. Exactly which file I have to look to overcome this errors. Go to the line number in the .top indicated in the error message and determine the atom types. This will tell you the sequence of atom types involved in the R-B dihedral that is missing. In theory, you would then add missing parameters to ffbonded.itp, if they exist. -Justin On Tue, Sep 10, 2013 at 8:25 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 9:21 AM, Rama Krishna Koppisetti wrote: Hi Justin, This is another type of error while running energy minimization: what to do for these type of errors. They're exactly the same as the dihedral error from before. You're using parameters that don't exist in the force field. -Justin ERROR 218 [file topol.top, line 23487]: No default Ryckaert-Bell. types ERROR 219 [file topol.top, line 23499]: No default Ryckaert-Bell. types ERROR 220 [file topol.top, line 23500]: No default Ryckaert-Bell. types ERROR 221 [file topol.top, line 23501]: No default Ryckaert-Bell. types ERROR 222 [file topol.top, line 23502]: No default Ryckaert-Bell. types ERROR 223 [file topol.top, line 23503]: No default Ryckaert-Bell. types ERROR 224 [file topol.top, line 23515]: No default Ryckaert-Bell. types --Rama On Mon, Sep 9, 2013 at 5:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/9/13 6:11 PM, Rama Krishna Koppisetti wrote: Hi Justin, I included 1 DMPC molecule parameters in the file should I need to include 128 molecules parameters in the file .rtp. No. Residue definitions are used any time they are encountered in the coordinate file. There is no need for such redundancy at the force field level. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalemkul@outerbanks.** umaryland.edu jalemkul@outerbanks.**umaryland.edujalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/**mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/**listinfo/gmx-users h**ttp://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search**h**ttp://www.gromacs.org/**Support/**http://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://**www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists http://**www.gromacs.org/**Support/**Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/**Support/**Mailing_Listshttp://www.gromacs.org/Support/**Mailing_Lists http:/**/www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users *
Re: [gmx-users] NMR restrained MD
On 9/10/13 1:28 PM, Rafael I. Silverman y de la Vega wrote: Adding parameters can be a little bit of a pain, you could instead change the atom types in the molecule parameter, to ones that have defined angles and bond types with each other. Of course, you would need to make sure that you dont assign sp2 with sp3 atoms, or aromatic with non aromatic etc. Check out ffbonded in the appropriate forcefield folder to see which atomtypes have defined bond types. Check out atomtypes.atp to see all the atom types for the forcefield Given that at present the issue involves only protein and lipids, the approach of swapping around atom types is very dangerous, probably more so than assigning bonded parameters by analogy. I don't recall the OP ever telling us what the force field is, though, so it's hard to know all of what we're dealing with here. -Justin On Tue, Sep 10, 2013 at 6:40 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 9:33 AM, Rama Krishna Koppisetti wrote: Hi Justin, It is which part in the force field. Exactly which file I have to look to overcome this errors. Go to the line number in the .top indicated in the error message and determine the atom types. This will tell you the sequence of atom types involved in the R-B dihedral that is missing. In theory, you would then add missing parameters to ffbonded.itp, if they exist. -Justin On Tue, Sep 10, 2013 at 8:25 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 9:21 AM, Rama Krishna Koppisetti wrote: Hi Justin, This is another type of error while running energy minimization: what to do for these type of errors. They're exactly the same as the dihedral error from before. You're using parameters that don't exist in the force field. -Justin ERROR 218 [file topol.top, line 23487]: No default Ryckaert-Bell. types ERROR 219 [file topol.top, line 23499]: No default Ryckaert-Bell. types ERROR 220 [file topol.top, line 23500]: No default Ryckaert-Bell. types ERROR 221 [file topol.top, line 23501]: No default Ryckaert-Bell. types ERROR 222 [file topol.top, line 23502]: No default Ryckaert-Bell. types ERROR 223 [file topol.top, line 23503]: No default Ryckaert-Bell. types ERROR 224 [file topol.top, line 23515]: No default Ryckaert-Bell. types --Rama On Mon, Sep 9, 2013 at 5:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/9/13 6:11 PM, Rama Krishna Koppisetti wrote: Hi Justin, I included 1 DMPC molecule parameters in the file should I need to include 128 molecules parameters in the file .rtp. No. Residue definitions are used any time they are encountered in the coordinate file. There is no need for such redundancy at the force field level. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalemkul@outerbanks.** umaryland.edu jalemkul@outerbanks.**umaryland.edujalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/**mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/**listinfo/gmx-users h**ttp://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search**h**ttp://www.gromacs.org/**Support/**http://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://**www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists http://**www.gromacs.org/**Support/**Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/**Support/**Mailing_Listshttp://www.gromacs.org/Support/**Mailing_Lists http:/**/www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu | (410)
[gmx-users] Freeze + NPT + constraints
Hi, Sorry to bother you again regarding this. But I am not sure, as to why freeze + constraints should not work during a NPT simulation? The update algorithm as shown in the manual does not say anything that would fundamentally prevent this. In fact, one can use freezegroups + constraints in NVT. What prevents it from running in NPT? I get the foll. error. step 0 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Warning: Triclinic box is too skewed. Warning: Triclinic box is too skewed. Warning: Triclinic box is too skewed. ... ... ... Segmentation fault -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NMR restrained MD
On 9/10/13 3:55 PM, Rama Krishna Koppisetti wrote: Hi Justin, There is no errors in dihedral but I got 4 warnings in ffbonded.itp. Is there any suggestions from you. You've constructed the force field such that you have repeating entries that override parameters. You still haven't said what force field you are using or how you constructed it, though it appears you are probably using some version of Berger parameters, if the atom types are any indication. -Justin WARNING 1 [file ffbonded.itp, line 2817]: Overriding Proper Dih. parameters. Use dihedraltype 4 to allow several multiplicity terms. old: 180 5.86 1 180 5.86 1 new: LNL LH2 LC2 LOS1 0.00 8.623 WARNING 2 [file ffbonded.itp, line 2820]: Overriding Proper Dih. parameters. Use dihedraltype 4 to allow several multiplicity terms. old: 0 5.09 2 0 5.09 2 new: LC2 LOSLP LOS1 0.00 3.193 WARNING 3 [file ffbonded.itp, line 2821]: Overriding Proper Dih. parameters. Use dihedraltype 4 to allow several multiplicity terms. old: 0 3.19 3 0 3.19 3 new: LOSLP LOS LC21 0.00 5.092 WARNING 4 [file ffbonded.itp, line 2822]: Overriding Proper Dih. parameters. Use dihedraltype 4 to allow several multiplicity terms. old: 0 5.09 2 0 5.09 2 new: LOSLP LOS LC21 0.00 3.193 Thanks --Rama On Tue, Sep 10, 2013 at 12:34 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 1:28 PM, Rafael I. Silverman y de la Vega wrote: Adding parameters can be a little bit of a pain, you could instead change the atom types in the molecule parameter, to ones that have defined angles and bond types with each other. Of course, you would need to make sure that you dont assign sp2 with sp3 atoms, or aromatic with non aromatic etc. Check out ffbonded in the appropriate forcefield folder to see which atomtypes have defined bond types. Check out atomtypes.atp to see all the atom types for the forcefield Given that at present the issue involves only protein and lipids, the approach of swapping around atom types is very dangerous, probably more so than assigning bonded parameters by analogy. I don't recall the OP ever telling us what the force field is, though, so it's hard to know all of what we're dealing with here. -Justin On Tue, Sep 10, 2013 at 6:40 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 9:33 AM, Rama Krishna Koppisetti wrote: Hi Justin, It is which part in the force field. Exactly which file I have to look to overcome this errors. Go to the line number in the .top indicated in the error message and determine the atom types. This will tell you the sequence of atom types involved in the R-B dihedral that is missing. In theory, you would then add missing parameters to ffbonded.itp, if they exist. -Justin On Tue, Sep 10, 2013 at 8:25 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 9:21 AM, Rama Krishna Koppisetti wrote: Hi Justin, This is another type of error while running energy minimization: what to do for these type of errors. They're exactly the same as the dihedral error from before. You're using parameters that don't exist in the force field. -Justin ERROR 218 [file topol.top, line 23487]: No default Ryckaert-Bell. types ERROR 219 [file topol.top, line 23499]: No default Ryckaert-Bell. types ERROR 220 [file topol.top, line 23500]: No default Ryckaert-Bell. types ERROR 221 [file topol.top, line 23501]: No default Ryckaert-Bell. types ERROR 222 [file topol.top, line 23502]: No default Ryckaert-Bell. types ERROR 223 [file topol.top, line 23503]: No default Ryckaert-Bell. types ERROR 224 [file topol.top, line 23515]: No default Ryckaert-Bell. types --Rama On Mon, Sep 9, 2013 at 5:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/9/13 6:11 PM, Rama Krishna Koppisetti wrote: Hi Justin, I included 1 DMPC molecule parameters in the file should I need to include 128 molecules parameters in the file .rtp. No. Residue definitions are used any time they are encountered in the coordinate file. There is no need for such redundancy at the force field level. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalemkul@outerbanks.**umaryla**nd.eduhttp://umaryland.edu jalemkul@outerbanks.**umaryland.edujalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org
Re: [gmx-users] NMR restrained MD
How so? If there is an atom type that has a reasonable similarity to the one that doesnt have the default bondtypes, what makes using that worse than coming up with entirely new parameters that are not necessarily based on physical data or quantum calculations? Isnt copying angles and force constants the same thing? On Tue, Sep 10, 2013 at 10:34 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 1:28 PM, Rafael I. Silverman y de la Vega wrote: Adding parameters can be a little bit of a pain, you could instead change the atom types in the molecule parameter, to ones that have defined angles and bond types with each other. Of course, you would need to make sure that you dont assign sp2 with sp3 atoms, or aromatic with non aromatic etc. Check out ffbonded in the appropriate forcefield folder to see which atomtypes have defined bond types. Check out atomtypes.atp to see all the atom types for the forcefield Given that at present the issue involves only protein and lipids, the approach of swapping around atom types is very dangerous, probably more so than assigning bonded parameters by analogy. I don't recall the OP ever telling us what the force field is, though, so it's hard to know all of what we're dealing with here. -Justin On Tue, Sep 10, 2013 at 6:40 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 9:33 AM, Rama Krishna Koppisetti wrote: Hi Justin, It is which part in the force field. Exactly which file I have to look to overcome this errors. Go to the line number in the .top indicated in the error message and determine the atom types. This will tell you the sequence of atom types involved in the R-B dihedral that is missing. In theory, you would then add missing parameters to ffbonded.itp, if they exist. -Justin On Tue, Sep 10, 2013 at 8:25 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 9:21 AM, Rama Krishna Koppisetti wrote: Hi Justin, This is another type of error while running energy minimization: what to do for these type of errors. They're exactly the same as the dihedral error from before. You're using parameters that don't exist in the force field. -Justin ERROR 218 [file topol.top, line 23487]: No default Ryckaert-Bell. types ERROR 219 [file topol.top, line 23499]: No default Ryckaert-Bell. types ERROR 220 [file topol.top, line 23500]: No default Ryckaert-Bell. types ERROR 221 [file topol.top, line 23501]: No default Ryckaert-Bell. types ERROR 222 [file topol.top, line 23502]: No default Ryckaert-Bell. types ERROR 223 [file topol.top, line 23503]: No default Ryckaert-Bell. types ERROR 224 [file topol.top, line 23515]: No default Ryckaert-Bell. types --Rama On Mon, Sep 9, 2013 at 5:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/9/13 6:11 PM, Rama Krishna Koppisetti wrote: Hi Justin, I included 1 DMPC molecule parameters in the file should I need to include 128 molecules parameters in the file .rtp. No. Residue definitions are used any time they are encountered in the coordinate file. There is no need for such redundancy at the force field level. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalemkul@outerbanks.**umaryla**nd.eduhttp://umaryland.edu jalemkul@outerbanks.**umaryland.edujalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users ht**tp://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users htt**p://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users h**ttp://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/**mailman/**listinfo/gmx-users h**ttp://lists.gromacs.org/**mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/**listinfo/gmx-users h**ttp://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/ Support/** http://www.gromacs.org/**Support/**http://www.gromacs. **org/Support/**
Re: [gmx-users] NMR restrained MD
Hi Justin, There is no errors in dihedral but I got 4 warnings in ffbonded.itp. Is there any suggestions from you. WARNING 1 [file ffbonded.itp, line 2817]: Overriding Proper Dih. parameters. Use dihedraltype 4 to allow several multiplicity terms. old: 180 5.86 1 180 5.86 1 new: LNL LH2 LC2 LOS1 0.00 8.623 WARNING 2 [file ffbonded.itp, line 2820]: Overriding Proper Dih. parameters. Use dihedraltype 4 to allow several multiplicity terms. old: 0 5.09 2 0 5.09 2 new: LC2 LOSLP LOS1 0.00 3.193 WARNING 3 [file ffbonded.itp, line 2821]: Overriding Proper Dih. parameters. Use dihedraltype 4 to allow several multiplicity terms. old: 0 3.19 3 0 3.19 3 new: LOSLP LOS LC21 0.00 5.092 WARNING 4 [file ffbonded.itp, line 2822]: Overriding Proper Dih. parameters. Use dihedraltype 4 to allow several multiplicity terms. old: 0 5.09 2 0 5.09 2 new: LOSLP LOS LC21 0.00 3.193 Thanks --Rama On Tue, Sep 10, 2013 at 12:34 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 1:28 PM, Rafael I. Silverman y de la Vega wrote: Adding parameters can be a little bit of a pain, you could instead change the atom types in the molecule parameter, to ones that have defined angles and bond types with each other. Of course, you would need to make sure that you dont assign sp2 with sp3 atoms, or aromatic with non aromatic etc. Check out ffbonded in the appropriate forcefield folder to see which atomtypes have defined bond types. Check out atomtypes.atp to see all the atom types for the forcefield Given that at present the issue involves only protein and lipids, the approach of swapping around atom types is very dangerous, probably more so than assigning bonded parameters by analogy. I don't recall the OP ever telling us what the force field is, though, so it's hard to know all of what we're dealing with here. -Justin On Tue, Sep 10, 2013 at 6:40 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 9:33 AM, Rama Krishna Koppisetti wrote: Hi Justin, It is which part in the force field. Exactly which file I have to look to overcome this errors. Go to the line number in the .top indicated in the error message and determine the atom types. This will tell you the sequence of atom types involved in the R-B dihedral that is missing. In theory, you would then add missing parameters to ffbonded.itp, if they exist. -Justin On Tue, Sep 10, 2013 at 8:25 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 9:21 AM, Rama Krishna Koppisetti wrote: Hi Justin, This is another type of error while running energy minimization: what to do for these type of errors. They're exactly the same as the dihedral error from before. You're using parameters that don't exist in the force field. -Justin ERROR 218 [file topol.top, line 23487]: No default Ryckaert-Bell. types ERROR 219 [file topol.top, line 23499]: No default Ryckaert-Bell. types ERROR 220 [file topol.top, line 23500]: No default Ryckaert-Bell. types ERROR 221 [file topol.top, line 23501]: No default Ryckaert-Bell. types ERROR 222 [file topol.top, line 23502]: No default Ryckaert-Bell. types ERROR 223 [file topol.top, line 23503]: No default Ryckaert-Bell. types ERROR 224 [file topol.top, line 23515]: No default Ryckaert-Bell. types --Rama On Mon, Sep 9, 2013 at 5:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/9/13 6:11 PM, Rama Krishna Koppisetti wrote: Hi Justin, I included 1 DMPC molecule parameters in the file should I need to include 128 molecules parameters in the file .rtp. No. Residue definitions are used any time they are encountered in the coordinate file. There is no need for such redundancy at the force field level. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalemkul@outerbanks.**umaryla**nd.eduhttp://umaryland.edu jalemkul@outerbanks.**umaryland.edujalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users ht**tp://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users htt**p://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users
Re: [gmx-users] NMR restrained MD
On 9/10/13 3:54 PM, Rafael I. Silverman y de la Vega wrote: How so? If there is an atom type that has a reasonable similarity to the one that doesnt have the default bondtypes, what makes using that worse than coming up with entirely new parameters that are not necessarily based on physical data or quantum calculations? Isnt copying angles and force constants the same thing? I never suggested that one should make up parameters that aren't based on anything. The nonbonded parameters of any force field are highly tuned for internal consistency, so I was alarmed at the suggestion of simply replacing atom types. Doing so can very easily perturb the model physics in unpredictable ways. Perhaps I should have stated more clearly from the beginning - I never meant to imply that anyone should simply add parameters for a missing interaction. They must be properly derived. I do maintain (having seen the negative consequences myself from others' struggles and failed attempts) that replacing atom types for mere convenience leads to very bad outcomes, probably just as bad as poorly concocted bonded parameters, if not worse. It should also be noted that the nonbonded parameters affect torsions, so all of these terms are, in reality, interrelated. I suspect that the underlying issue here has been a poorly constructed force field, not parameters that are actually missing from the model. -Justin On Tue, Sep 10, 2013 at 10:34 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 1:28 PM, Rafael I. Silverman y de la Vega wrote: Adding parameters can be a little bit of a pain, you could instead change the atom types in the molecule parameter, to ones that have defined angles and bond types with each other. Of course, you would need to make sure that you dont assign sp2 with sp3 atoms, or aromatic with non aromatic etc. Check out ffbonded in the appropriate forcefield folder to see which atomtypes have defined bond types. Check out atomtypes.atp to see all the atom types for the forcefield Given that at present the issue involves only protein and lipids, the approach of swapping around atom types is very dangerous, probably more so than assigning bonded parameters by analogy. I don't recall the OP ever telling us what the force field is, though, so it's hard to know all of what we're dealing with here. -Justin On Tue, Sep 10, 2013 at 6:40 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 9:33 AM, Rama Krishna Koppisetti wrote: Hi Justin, It is which part in the force field. Exactly which file I have to look to overcome this errors. Go to the line number in the .top indicated in the error message and determine the atom types. This will tell you the sequence of atom types involved in the R-B dihedral that is missing. In theory, you would then add missing parameters to ffbonded.itp, if they exist. -Justin On Tue, Sep 10, 2013 at 8:25 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 9:21 AM, Rama Krishna Koppisetti wrote: Hi Justin, This is another type of error while running energy minimization: what to do for these type of errors. They're exactly the same as the dihedral error from before. You're using parameters that don't exist in the force field. -Justin ERROR 218 [file topol.top, line 23487]: No default Ryckaert-Bell. types ERROR 219 [file topol.top, line 23499]: No default Ryckaert-Bell. types ERROR 220 [file topol.top, line 23500]: No default Ryckaert-Bell. types ERROR 221 [file topol.top, line 23501]: No default Ryckaert-Bell. types ERROR 222 [file topol.top, line 23502]: No default Ryckaert-Bell. types ERROR 223 [file topol.top, line 23503]: No default Ryckaert-Bell. types ERROR 224 [file topol.top, line 23515]: No default Ryckaert-Bell. types --Rama On Mon, Sep 9, 2013 at 5:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/9/13 6:11 PM, Rama Krishna Koppisetti wrote: Hi Justin, I included 1 DMPC molecule parameters in the file should I need to include 128 molecules parameters in the file .rtp. No. Residue definitions are used any time they are encountered in the coordinate file. There is no need for such redundancy at the force field level. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalemkul@outerbanks.**umaryla**nd.eduhttp://umaryland.edu jalemkul@outerbanks.**umaryland.edujalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org
Re: [gmx-users] Freeze + NPT + constraints
On 9/10/13 2:59 PM, HANNIBAL LECTER wrote: Hi, Sorry to bother you again regarding this. But I am not sure, as to why freeze + constraints should not work during a NPT simulation? The update algorithm as shown in the manual does not say anything that would fundamentally prevent this. In fact, one can use freezegroups + constraints in NVT. What prevents it from running in NPT? The use of a barostat requires that the positions of the atoms can be scaled according to the pressure. Freezing atoms, by definition, makes them immobile and thus they cannot be scaled. Thus, the two algorithms are fundamentally incompatible. -Justin I get the foll. error. step 0 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Warning: Triclinic box is too skewed. Warning: Triclinic box is too skewed. Warning: Triclinic box is too skewed. ... ... ... Segmentation fault -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: plans for mdrun features to deprecate in GROMACS 5.0
Hi, The near-silence has been deafening, so these issues are regarded as closed. Anybody wanting a significant deviation from that plan will find the onus on them to do the work! :-) Cheers, Mark On Wed, Aug 14, 2013 at 5:06 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi gmx-users and gmx-developers, There are a number of features of GROMACS that we plan to drop for 5.0 (scheduled for early 2014). We don’t like doing this, but if things are broken or cause developers pain, then they will go unless there is manpower to support them. We’d like to keep you informed and hear how much pain any of this might cause. Some features will be dropped entirely, and others are likely to be reduced to explicit support only for some cases. Some discussion has already occurred here http://redmine.gromacs.org/issues/1292. Things we plan to drop entirely: * particle decomposition (see below) * current QM support (this will be dropped, work on a replacement is underway, planned for 5.0) * writing of pair distance and/or time-averaged pair distance to energy files during simulations with position/orientation restraints * reaction-field-nec * Encad-shift * mdrun -ionize * GCT * mdrun -seppot * mdrun -ffscan * OpenMM support There are several algorithms (e.g. fancy kinds of restraints) that have only ever worked with particle decomposition (if they work at all...). We plan to support these only in serial. Things that will likely only work in serial (ie. single-domain DD): * ensemble- and time-averaged distance restraints * L-BFGS energy minimization * Generalized Born In some cases, “in serial” might mean “in parallel (with DD) with an extra communication stage that will make it work, but might scale poorly.” Or “in parallel but if things diffuse too far, the simulation will crash.” If you have working examples of any of the above in parallel, we would be most interested to hear from you. We’d like to construct test cases that show what works now, so that later if we are able to support some kind of parallelism, we can show that it still works. Things that won’t support constraints (because the implementations are broken or missing): * L-BFGS energy minimization * MTTK pressure coupling As always, what goes into GROMACS depends on people putting the work in. If something above would affect you, then do speak up. Contributions of working test cases are particularly valuable, but in the end you might have to be the one to write the code to make the test pass. You will have the option of continuing to use old code, too! Cheers, Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Freeze + NPT + constraints
I would think that too. However, that is not what happens. If you freeze a group it gets scaled according to the box vectors during a npt simulation. Hence in order to keep the group (in my case a carbon nano tube) of fixed diameter i use position restraints. This protocol works fine with with npt simulations. Now, i wanted to check if i include the bonded interactions in my topology and constrain all the bonds things should not matter at all, since the bonded interactions are redundant in this case. However, that is not the case and the system crashes. If however the bonds are not constrained, things work fine. I know this is a very round about way of getting things done, still i am curious. On Sep 10, 2013 4:12 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 2:59 PM, HANNIBAL LECTER wrote: Hi, Sorry to bother you again regarding this. But I am not sure, as to why freeze + constraints should not work during a NPT simulation? The update algorithm as shown in the manual does not say anything that would fundamentally prevent this. In fact, one can use freezegroups + constraints in NVT. What prevents it from running in NPT? The use of a barostat requires that the positions of the atoms can be scaled according to the pressure. Freezing atoms, by definition, makes them immobile and thus they cannot be scaled. Thus, the two algorithms are fundamentally incompatible. -Justin I get the foll. error. step 0 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Warning: Triclinic box is too skewed. Warning: Triclinic box is too skewed. Warning: Triclinic box is too skewed. ... ... ... Segmentation fault -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Freeze + NPT + constraints
On 9/10/13 5:17 PM, HANNIBAL LECTER wrote: I would think that too. However, that is not what happens. If you freeze a group it gets scaled according to the box vectors during a npt simulation. Are the positions of the atoms actually changing? If they are, that's a bug. It shouldn't happen, and in previous version of Gromacs, I know it didn't. Can you point to the code that is making this happen? Hence in order to keep the group (in my case a carbon nano tube) of fixed diameter i use position restraints. This protocol works fine with with npt simulations. Now, i wanted to check if i include the bonded interactions in my topology and constrain all the bonds things should not matter at all, since the bonded interactions are redundant in this case. However, that is not the case and the system crashes. If however the bonds are not constrained, things work fine. I know this is a very round about way of getting things done, still i am curious. Constraints and barostats both try to modify coordinates. The freezegrps mechanism prevents modifications of coordinates, so what you're trying to satisfy is a barostat that wants to scale coordinates (you say that is accomplished somehow; I would like to see the evidence so the issue can be addressed) and a constraint algorithm that wants to satisfy bond lengths. One of those is bound to fail. I can imagine that if the initial configuration perfectly satisfied the constraints, then maybe the run could proceed (because freezegrps and constraints wouldn't be fighting one another), but I still can't get my head around any way that you could satisfy freezing and a barostat. In reality, what we should do is make it a fatal error, because truly, frozen groups should be used very sparingly and certainly never with NPT. It just doesn't make sense. I understand what you're trying to accomplish, but the underlying theory becomes flawed. -Justin On Sep 10, 2013 4:12 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 2:59 PM, HANNIBAL LECTER wrote: Hi, Sorry to bother you again regarding this. But I am not sure, as to why freeze + constraints should not work during a NPT simulation? The update algorithm as shown in the manual does not say anything that would fundamentally prevent this. In fact, one can use freezegroups + constraints in NVT. What prevents it from running in NPT? The use of a barostat requires that the positions of the atoms can be scaled according to the pressure. Freezing atoms, by definition, makes them immobile and thus they cannot be scaled. Thus, the two algorithms are fundamentally incompatible. -Justin I get the foll. error. step 0 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23 -2.7758e+23 Warning: Triclinic box is too skewed. Warning: Triclinic box is too skewed. Warning: Triclinic box is too skewed. ... ... ... Segmentation fault -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at
Re: [gmx-users] NMR restrained MD
On 9/10/13 4:35 PM, Rama Krishna Koppisetti wrote: H i Justin, The force field that I constructed with OPLS + Berger lipids . Similar to your Bilayer tutorial. Presumably you are following Chris Neale's half-epsilon, double pairlist method then? In any case, you're defining the same interaction multiple times using different parameters. Something has gone wrong somewhere along the way. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NMR restrained MD
Hi, How to convert normal dihedrals to so-called Ryckaert-Bellemans potential dihedrals. Is there any script available for that. Thanks Rama On Tue, Sep 10, 2013 at 3:44 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 4:35 PM, Rama Krishna Koppisetti wrote: H i Justin, The force field that I constructed with OPLS + Berger lipids . Similar to your Bilayer tutorial. Presumably you are following Chris Neale's half-epsilon, double pairlist method then? In any case, you're defining the same interaction multiple times using different parameters. Something has gone wrong somewhere along the way. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NMR restrained MD
On 9/10/13 6:10 PM, Rama Krishna Koppisetti wrote: Hi, How to convert normal dihedrals to so-called Ryckaert-Bellemans potential dihedrals. Is there any script available for that. Periodic dihedrals and R-B dihedrals have different functional forms. See the manual. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] average pressure of a system
Hi All. I work on a simulation of a membrane protein in a model membrane (DPPC) with a total of 26,859 atoms. In a step of NPT equilibration, my mdp file is used for a 100 ps NPT and it has a reference pressure of 1 bar. At the end of simulation, I obtained a result of the average pressure of the system ( ~ -0.90 bar) like Energy Average Err.Est. RMSD Tot-Drift --- Pressure-0.90492.6186.30413.8503 (bar) I am wondering if I should keep running this NPT process until the average pressure of the system reaches ~ 1.0 bar. If so, how long ( how many steps) ? Or should I modify mdp file ? Can anyone provide some suggestions ? Likewise, at the end of Production MD for 1 ns, I obtained average pressure (~2.23 bar) of the system like Energy Average Err.Est. RMSD Tot-Drift --- Pressure2.233492.1 164.9710.9381 (bar) Should I run a longer simulation until the average pressure reaches ~ 1.0 bar, although average energy, average temperature (323 K), average density (1022 kg/m^3) are already at the desired values ? How should I do to stabilize average pressure at a desired value (~1 bar) ? Thanks for any input. Dwey -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NMR restrained MD
H i Justin, The force field that I constructed with OPLS + Berger lipids . Similar to your Bilayer tutorial. Thanks --Rama On Tue, Sep 10, 2013 at 3:26 PM, Rama Krishna Koppisetti ramkishn...@gmail.com wrote: -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] average pressure of a system
On 9/10/13 9:12 PM, Dwey wrote: Hi All. I work on a simulation of a membrane protein in a model membrane (DPPC) with a total of 26,859 atoms. In a step of NPT equilibration, my mdp file is used for a 100 ps NPT and it has a reference pressure of 1 bar. At the end of simulation, I obtained a result of the average pressure of the system ( ~ -0.90 bar) like Energy Average Err.Est. RMSD Tot-Drift --- Pressure-0.90492.6186.30413.8503 (bar) I am wondering if I should keep running this NPT process until the average pressure of the system reaches ~ 1.0 bar. If so, how long ( how many steps) ? Or should I modify mdp file ? Can anyone provide some suggestions ? If you want commentary on your .mdp file, you need to provide the actual .mdp file. Likewise, at the end of Production MD for 1 ns, I obtained average pressure (~2.23 bar) of the system like Energy Average Err.Est. RMSD Tot-Drift --- Pressure2.233492.1 164.9710.9381 (bar) Should I run a longer simulation until the average pressure reaches ~ 1.0 bar, although average energy, average temperature (323 K), average density (1022 kg/m^3) are already at the desired values ? How should I do to stabilize average pressure at a desired value (~1 bar) ? None of this looks abnormal to me at all. This topic is discussed very frequently on the list, so please refer to the archive for extensive discussion about the theory of pressure calculations and what the output means. Also have a look at http://www.gromacs.org/Documentation/Terminology/Pressure and ask yourself whether 2 ± 165 is significantly different from the target value of 1. Also realize the 1 ns is extremely short for a membrane system, which normally take tens of ns to equilibrate. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] average pressure of a system
Part answer is provided at http://www.gromacs.org/Documentation/Terminology/Pressure Have you plotted how the pressure changes with time during your simulation? What you will notice is that the pressure is oscillating between something like +300 bar and -300 bar. With such large variations like that, is it not surprising that the average is not exactly 1? Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Dwey Sent: Wednesday, 11 September 2013 11:12 AM To: gmx-users@gromacs.org Subject: [gmx-users] average pressure of a system Hi All. I work on a simulation of a membrane protein in a model membrane (DPPC) with a total of 26,859 atoms. In a step of NPT equilibration, my mdp file is used for a 100 ps NPT and it has a reference pressure of 1 bar. At the end of simulation, I obtained a result of the average pressure of the system ( ~ -0.90 bar) like Energy Average Err.Est. RMSD Tot-Drift --- Pressure-0.90492.6186.30413.8503 (bar) I am wondering if I should keep running this NPT process until the average pressure of the system reaches ~ 1.0 bar. If so, how long ( how many steps) ? Or should I modify mdp file ? Can anyone provide some suggestions ? Likewise, at the end of Production MD for 1 ns, I obtained average pressure (~2.23 bar) of the system like Energy Average Err.Est. RMSD Tot-Drift --- Pressure2.233492.1 164.9710.9381 (bar) Should I run a longer simulation until the average pressure reaches ~ 1.0 bar, although average energy, average temperature (323 K), average density (1022 kg/m^3) are already at the desired values ? How should I do to stabilize average pressure at a desired value (~1 bar) ? Thanks for any input. Dwey -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RE: average pressure of a system
Hi Dallas and Justin, Thanks for the reply. Yes, I did plot pressure changes over time by g_energy and I have been aware of the note at http://www.gromacs.org/Documentation/Terminology/Pressure I am concerned about the average pressure is because our experiment shows that our target membrane protein is a hexamer and our observation is that variation of system pressure seems causing hexamer or dimer dissociation. Also, it is quite sensitive to pressure fluctuation. Such a fluctuation of pressure certainly brings my attention in this specific case, because life does not exist at large variations of system pressure. If not because of multimer dissociation likely caused by pressure fluctuation, I agree with both of you. I also run longer simulations like 20 ns and 30 ns ### 20 ns Energy Average Err.Est. RMSD Tot-Drift --- Pressure 0.886396 0.84162.6551.38476 (bar) ## 30 ns Energy Average Err.Est. RMSD Tot-Drift --- Pressure1.69086 0.58162.8793.35668 (bar) Running longer simulations seems to me that the improvement of system pressure is not helpful too much. If I need to modify mdp file, what it would be ? Many thanks, Dwey My mdp file for NPT is used in the simulation like define = -DPOSRES integrator = md nsteps = 50 dt = 0.002 nstxout = 100 nstvout = 100 nstenergy = 100 nstlog = 100 continuation= yes constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 4 ns_type = grid nstlist = 5 rlist = 1.2 rcoulomb= 1.2 rvdw= 1.2 coulombtype = PME pme_order = 4 fourierspacing = 0.16 tcoupl = Nose-Hoover tc-grps = Protein DPPC SOL_CL tau_t = 0.5 0.5 0.5 ref_t = 323 323 323 pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 5.0 ref_p = 1.0 1.0 compressibility = 4.5e-54.5e-5 pbc = xyz DispCorr= EnerPres gen_vel = no nstcomm = 1 comm-mode = Linear comm-grps = Protein_DPPC SOL_CL refcoord_scaling = com cutoff-scheme = Verlet -- View this message in context: http://gromacs.5086.x6.nabble.com/average-pressure-of-a-system-tp5011095p5011098.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] ERROR while compiling gromacs4.6.1
Hello, i am trying to compile gromacs-4.6.1 on a linux machine. I used already the following compile script and it worked export CCDIR=/usr/bin/gcc export MPICCDIR=/usr/mpi/gcc/openmpi-1.4.1/bin export CXX=mpicxx export CC=mpicc cd /home/fbafti/CODE tar -xvf gromacs-4.6.1.tar.gz cd mv gromacs-4.6.1 gromacs-4.6.1-plumed/ cd build-gromacs-4.6.1-plumed/ /home/fbafti/CODE/cmake-2.8.11.2-Linux-i386/bin/cmake /home/fbafti/CODE/gromacs-4.6.1-plumed \ -DFFTWF_LIBRARY=/home/fbafti/CODE/fftw-3.3.3/lib/libfftw3f.so \ -DFFTW3F_INCLUDE_DIR=/home/fbafti/CODE/fftw-3.3.3/include \ -DFFTW3F_LIBRARIES=/home/fbafti/CODE/fftw-3.3.3/lib/libfftw3f.a \ -DCMAKE_INSTALL_PREFIX=/home/fbafti/CODE/build-gromacs-4.6.1-plumed \ -DGMX_X11=OFF \ -DCMAKE_CXX_COMPILER=/usr/mpi/gcc/openmpi-1.4.1/bin/mpicxx \ -DCMAKE_C_COMPILER=/usr/mpi/gcc/openmpi-1.4.1/bin/mpicc \ -DGMX_MPI=ON \ -DGMX_PREFER_STATIC_LIBS=ON However I am trying it now on another machine with the same linux platform and I get the following error: CMake Warning at CMakeLists.txt:727 (message): No C SSE4.1 flag found. Consider a newer compiler, or use SSE2 for slightly lower performance -- Looking for smmintrin.h -- Looking for smmintrin.h - not found CMake Error at CMakeLists.txt:750 (message): Cannot find smmintrin.h, which is required for SSE4.1 intrinsics support. -- Configuring incomplete, errors occurred! I thought if the gcc path is already defined ... it shouldn't complain ! Can you help me figure out what causes the error? Many thanks G. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] RE: average pressure of a system
On 9/10/13 10:56 PM, Dwey Kauffman wrote: Hi Dallas and Justin, Thanks for the reply. Yes, I did plot pressure changes over time by g_energy and I have been aware of the note at http://www.gromacs.org/Documentation/Terminology/Pressure I am concerned about the average pressure is because our experiment shows that our target membrane protein is a hexamer and our observation is that variation of system pressure seems causing hexamer or dimer dissociation. Also, it is quite sensitive to pressure fluctuation. Such a fluctuation of pressure certainly brings my attention in this specific case, because life does not exist at large variations of system pressure. True, but thermostats allow temperatures to oscillate on the order of a few K, and that doesn't happen on the macroscopic level either. Hence the small disconnect between a system that has thousands of atoms and one that has millions or trillions. Pressure fluctuations decrease on the order of sqrt(N), so the system size itself is a determining factor for the pressure fluctuations. As previous discussions have rightly concluded, pressure is a somewhat ill-defined quantity in molecular systems like these. If not because of multimer dissociation likely caused by pressure fluctuation, I agree with both of you. I also run longer simulations like 20 ns and 30 ns ### 20 ns Energy Average Err.Est. RMSD Tot-Drift --- Pressure 0.886396 0.84162.6551.38476 (bar) ## 30 ns Energy Average Err.Est. RMSD Tot-Drift --- Pressure1.69086 0.58162.8793.35668 (bar) Running longer simulations seems to me that the improvement of system pressure is not helpful too much. And yet neither is statistically indistinguishable from the value of 1, given that the standard deviations are ~163 bar. If I need to modify mdp file, what it would be ? You could try altering tau_p, but I doubt there is any value in doing so. -Justin Many thanks, Dwey My mdp file for NPT is used in the simulation like define = -DPOSRES integrator = md nsteps = 50 dt = 0.002 nstxout = 100 nstvout = 100 nstenergy = 100 nstlog = 100 continuation= yes constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 4 ns_type = grid nstlist = 5 rlist = 1.2 rcoulomb= 1.2 rvdw= 1.2 coulombtype = PME pme_order = 4 fourierspacing = 0.16 tcoupl = Nose-Hoover tc-grps = Protein DPPC SOL_CL tau_t = 0.5 0.5 0.5 ref_t = 323 323 323 pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 5.0 ref_p = 1.0 1.0 compressibility = 4.5e-54.5e-5 pbc = xyz DispCorr= EnerPres gen_vel = no nstcomm = 1 comm-mode = Linear comm-grps = Protein_DPPC SOL_CL refcoord_scaling = com cutoff-scheme = Verlet -- View this message in context: http://gromacs.5086.x6.nabble.com/average-pressure-of-a-system-tp5011095p5011098.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] RE: average pressure of a system
Also remember that here you are dealing with the measurement of a macroscopic property on a microscopic scale. As Justin has alluded to, the only manner in which you can make the variation / fluctuations in the pressure smaller is by increase the total number of particles in the system. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Dwey Kauffman Sent: Wednesday, 11 September 2013 12:57 PM To: gmx-users@gromacs.org Subject: [gmx-users] RE: average pressure of a system Hi Dallas and Justin, Thanks for the reply. Yes, I did plot pressure changes over time by g_energy and I have been aware of the note at http://www.gromacs.org/Documentation/Terminology/Pressure I am concerned about the average pressure is because our experiment shows that our target membrane protein is a hexamer and our observation is that variation of system pressure seems causing hexamer or dimer dissociation. Also, it is quite sensitive to pressure fluctuation. Such a fluctuation of pressure certainly brings my attention in this specific case, because life does not exist at large variations of system pressure. If not because of multimer dissociation likely caused by pressure fluctuation, I agree with both of you. I also run longer simulations like 20 ns and 30 ns ### 20 ns Energy Average Err.Est. RMSD Tot-Drift --- Pressure 0.886396 0.84162.6551.38476 (bar) ## 30 ns Energy Average Err.Est. RMSD Tot-Drift --- Pressure1.69086 0.58162.8793.35668 (bar) Running longer simulations seems to me that the improvement of system pressure is not helpful too much. If I need to modify mdp file, what it would be ? Many thanks, Dwey My mdp file for NPT is used in the simulation like define = -DPOSRES integrator = md nsteps = 50 dt = 0.002 nstxout = 100 nstvout = 100 nstenergy = 100 nstlog = 100 continuation= yes constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 4 ns_type = grid nstlist = 5 rlist = 1.2 rcoulomb= 1.2 rvdw= 1.2 coulombtype = PME pme_order = 4 fourierspacing = 0.16 tcoupl = Nose-Hoover tc-grps = Protein DPPC SOL_CL tau_t = 0.5 0.5 0.5 ref_t = 323 323 323 pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 5.0 ref_p = 1.0 1.0 compressibility = 4.5e-54.5e-5 pbc = xyz DispCorr= EnerPres gen_vel = no nstcomm = 1 comm-mode = Linear comm-grps = Protein_DPPC SOL_CL refcoord_scaling = com cutoff-scheme = Verlet -- View this message in context: http://gromacs.5086.x6.nabble.com/average-pressure-of-a-system- tp5011095p5011098.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RE: average pressure of a system
True, but thermostats allow temperatures to oscillate on the order of a few K, and that doesn't happen on the macroscopic level either. Hence the small disconnect between a system that has thousands of atoms and one that has millions or trillions. Pressure fluctuations decrease on the order of sqrt(N), so the system size itself is a determining factor for the pressure fluctuations. As previous discussions have rightly concluded, pressure is a somewhat ill-defined quantity in molecular systems like these. Dose it also imply that it is not a good idea to study the relationship between dimer (multimer) dissociation and macroscopic pressure in this case ? (due to the ill defined pressure). It is hard to be justified if I assign a set of various ref_p= 0.7, 0.8, 0.9, 1.0, 1.1, 1.2 , perform independent simulations, and then obtain outcomes of targeted quantities for comparison. You could try altering tau_p, but I doubt there is any value in doing so. I would give it a try. Thanks for the hint. Dwey www interface or send it to gmx-users-request@. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- View this message in context: http://gromacs.5086.x6.nabble.com/average-pressure-of-a-system-tp5011095p5011102.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Error in Installing gromacs4.6.3 with mpi
Dear all, I'm trying to install gromacs4.6.3 with mvapich2-1.9a on a local cluster and got the following error in step 'make': /usr/bin/ld: /usr/local/mvapich2-1.9a-gcc/lib/libmpich.a(mvapich_malloc.o): relocation R_X86_64_32 against `.bss' can not be used when making a shared object; recompile with -fPIC /usr/local/mvapich2-1.9a-gcc/lib/libmpich.a: could not read symbols: Bad value I was using command cmake ../ -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/.../gromacs-4.6.3/ -DGMX_BUILD_OWN_FFTW=ON -BUILD_SHARED_LIBS='no' and I thought the mvapich is compiled with --enable-shared... Could you give me some advice if possible? Thanks in advance. Best Qin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Fwd: installing Gromacs4.6.3 on cygwin
Thanks Wahab I followed your instruction and added #define HAVE_SYS_TIME_H at the very top of the file gmxlib/thread_mpi/impl.h. Then again in make command I got following errors. [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_avx_256_double.c.o [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_avx_256_double.c.o [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_avx_256_double.c.o [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_avx_256_double.c.o [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomP1P1_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW3P1_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW3W3_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW4P1_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW4W4_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomP1P1_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3P1_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW4P1_avx_256_double.c.o [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW4W4_avx_256_double.c.o make[2]: *** No rule to make target `//cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a', needed by `src/gmxlib/cyggmx_d-8.dll'. Stop. CMakeFiles/Makefile2:1238: recipe for target `src/gmxlib/CMakeFiles/gmx.dir/all' failed make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 Makefile:146: recipe for target `all' failed make: *** [all] Error 2 Please help me to compile gromacs 4.6.3 on cygwin Shahid Nayeem On Tue, Sep 10, 2013 at 9:13 PM, Mirco Wahab mirco.wa...@chemie.tu-freiberg.de wrote: On 10.09.2013 08:20, shahid nayeem wrote: I am installing gromacs -4.6.3 on cygwin with following commands tar -xvzf gramcs-4.6.3.tar.gz cd gromacs-4.6.3 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_DOUBLE=on It runs fine and write file in build directory. when I run make command it gives following error. ... /cygdrive/c/packages/gromacs-**4.6.3/src/gmxlib/thread_mpi/** impl.h:504:20: error: field ‘timer_init’ has incomplete type struct timeval timer_init; ^ src/gmxlib/CMakeFiles/gmx.dir/**build.make:3070: recipe for target The Gromacs-file gmxlib/thread_mpi/impl.h is missing the correct #define for the unixish Cygwin pseudo-os. You can add it by inserting #define HAVE_SYS_TIME_H at the very top of the file gmxlib/thread_mpi/impl.h Then the package will probably compile and link, but mdrun's thread-mpi (tMPI) will not work on Cygwin (didn't work last time I tried). So you could do the following: 1) install the Gromacs package with normal compilation, and 2) build and install the openmpi-version of mdrun (mdrun_mpi). (1) cmake-options for package: ... -DGMX_GPU=OFF \ -DGMX_PREFER_STATIC_LIBS=ON \ ... make -j4 install (delete all files from the build path) (2) cmake options for mdrun_mpi ... -DGMX_GPU=OFF\ -DGMX_MPI=ON \ -DGMX_PREFER_STATIC_LIBS=ON \ ... make -j4 install-mdrun The openmpi-version (mdrun_mpi) runs reasonable on Cygwin/64 1.7.25, but not as fast as the native windows version (compiled with visual studio 10 or 12). The windows-compiled version of 4.6.3 is very robust and allows to link mdrun against CUDA 5.0 (but not 5.5(+VC12) for unknown reasons). Then, you'll have full gpu support under windows. Regards M. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**
