[gmx-users] Re: g_energy: Energy names magic number mismatch
Justin, Thanks a lot. Concatenation seems to be the only solution, but it works fine. It look like there are some problems with the appending routine on BlueGene. Mikhail Dear Justin and Berk, Thank you very much for the hint. Unfortunately, upgrade to 4.5.3 version doesn't solve the problem, diagnostic is still the same: == Program g_energy_d, VERSION 4.5.3 Source code file: ../../../src/gmxlib/enxio.c, line: 422 Fatal error: Energy names magic number mismatch, this is not a GROMACS edr file For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors === Do you think there could be any way to overcome this problem apart from running the job in parts? Just to clarify, now that you've upgraded to 4.5.3, are you also running the 4.5.3 version of mdrun, and not just analyzing a 4.5.1 .edr file with 4.5.3? I believe there have been changes to the .edr file format over the course of development. There are several things to try to better diagnose what's going on. If file appending isn't working properly, that would be a major problem. To diagnose: 1. What does gmxcheck tell you about the problematic .edr file? 2. Try running the jobs as separate intervals. Check the integrity of each with gmxcheck and concatenate them with eneconv. Then use gmxcheck on this manually concatenated .edr file. If g_energy works on this file, then the problem is in the appending routines, not the file format. -Justin Many thanks in advance, Mikhail Dear gromacs users, I am facing the following problem while running gromacs 4.5.1 at BlueGene/P supercomputer. The job is submitted by the following script file: #!/bin/sh # # @ account_no = xxx # @ job_name= NVT1 # @ job_type= bluegene # @ output = $(job_name).$(jobid).out # @ error = $(job_name).$(jobid).err # @ environment = COPY_ALL; # @ wall_clock_limit= 24:00:00 # @ notification= always # @ bg_size = 64 # @ queue ?/mpirun -cwd $PWD -mode VN -np 256 -exe ?/mdrun_bgp_d -args -deffnm nvt1 -dds 0.5 -cpi nvt1.cpt -append And it is running perfectly fine. I can analyze the data using g_energy etc. But if after the run is finished I increase the number of time steps and submit run again or resubmit it after a crash (killed manually or due to 24 hours wall clock limit), using the same script provided above, the run itself looks fine, at least .log file looks as it should but when I try to analyze .edr file with g_energy tool I obtain the following error message: --- Program g_energy_d, VERSION 4.5.1 Source code file: ../../../src/gmxlib/enxio.c, line: 409 Fatal error: Energy names magic number mismatch, this is not a GROMACS edr file For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I would really appreciate any hint on this subject. This was a Gromacs bug in versions 4.5.1 and 4.5.2. Please upgrade to version 4.5.3. http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x -Justin Many thanks in advance. Mikhail. -- 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] perl script for g_hbond
Dear Justin, I ran you H bond frequency script and I got the following result. I am understanding that the occupancy of H bonds is on the writeside, but somehow in donor and acceptor column there is the residue name not atom type. I am not quiet good iunderstanding my output. Please can you advice me on this? #DonorAcceptor % Exist. 0.040 LIG1C1 LIG1C2 0.680 LIG1H7 LIG1H9 0.040 0.040 LIG1N30.360 LIG1N20.120 LIG1O2 0.040 0.120 LIG1N1 LIG1O2 0.120 0.040 0.160 0.040 0.040 0.040 0.040 0.080 0.200 0.040 0.040 0.200 0.080 best, Olga 2010/11/29 Justin A. Lemkul jalem...@vt.edu Olga Ivchenko wrote: Hi Leila, I am also have a task to calculate H-bonds frequency through the over all trajectory in gromacs. Please can you send me Justin's script. If he does not mind. I have several analysis scripts available to the public on my website: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html -Justin Yours sincerely, Olga 2010/11/29 leila karami karami.lei...@gmail.com mailto: karami.lei...@gmail.com Dear Mark and gromacs users thanks for your time and consideration. you said by multiplying the existence functions for hbonds between protein and water and the hbonds between water and DNA, then using Justin's script, I can obtain percentage each water medited hydrogen bond during trajectory. and also you said I need to create a corresponding index file too. I don't know where should I start for multiply two existence functions? please explain about it more. any help will highly appreciated. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] HBOND probability
Hello Justin, I wanted to find the probability of hydrogen bond formed between my peptide and water molecules over time. So I used your plot_hbmap.pl script. As mentioned in the script file, my index file contained atom numbers only from the [hbonds...] section, rest were deleted. Heres my short output after running the script: #DonorAcceptor % Exist. 0.004 ALAA N 0.004 ALAA N 0.016 ALAA N 0.012 ALAA N 0.008 ALAA O 0.008 ASNA OD1 0.012 GLYA O 0.008 ALAA O 0.008 Please can I know if this is the expected output from the script ??? if not please can I know what might be wrong in my input Kind regards, chetan. Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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: g_energy: Energy names magic number mismatch
Mikhail Stukan wrote: Justin, Thanks a lot. Concatenation seems to be the only solution, but it works fine. It look like there are some problems with the appending routine on BlueGene. Please file a bugzilla so this issue gets fixed. -Justin Mikhail Dear Justin and Berk, Thank you very much for the hint. Unfortunately, upgrade to 4.5.3 version doesn't solve the problem, diagnostic is still the same: == Program g_energy_d, VERSION 4.5.3 Source code file: ../../../src/gmxlib/enxio.c, line: 422 Fatal error: Energy names magic number mismatch, this is not a GROMACS edr file For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors === Do you think there could be any way to overcome this problem apart from running the job in parts? Just to clarify, now that you've upgraded to 4.5.3, are you also running the 4.5.3 version of mdrun, and not just analyzing a 4.5.1 .edr file with 4.5.3? I believe there have been changes to the .edr file format over the course of development. There are several things to try to better diagnose what's going on. If file appending isn't working properly, that would be a major problem. To diagnose: 1. What does gmxcheck tell you about the problematic .edr file? 2. Try running the jobs as separate intervals. Check the integrity of each with gmxcheck and concatenate them with eneconv. Then use gmxcheck on this manually concatenated .edr file. If g_energy works on this file, then the problem is in the appending routines, not the file format. -Justin Many thanks in advance, Mikhail Dear gromacs users, I am facing the following problem while running gromacs 4.5.1 at BlueGene/P supercomputer. The job is submitted by the following script file: #!/bin/sh # # @ account_no = xxx # @ job_name= NVT1 # @ job_type= bluegene # @ output = $(job_name).$(jobid).out # @ error = $(job_name).$(jobid).err # @ environment = COPY_ALL; # @ wall_clock_limit= 24:00:00 # @ notification= always # @ bg_size = 64 # @ queue ?/mpirun -cwd $PWD -mode VN -np 256 -exe ?/mdrun_bgp_d -args -deffnm nvt1 -dds 0.5 -cpi nvt1.cpt -append And it is running perfectly fine. I can analyze the data using g_energy etc. But if after the run is finished I increase the number of time steps and submit run again or resubmit it after a crash (killed manually or due to 24 hours wall clock limit), using the same script provided above, the run itself looks fine, at least .log file looks as it should but when I try to analyze .edr file with g_energy tool I obtain the following error message: --- Program g_energy_d, VERSION 4.5.1 Source code file: ../../../src/gmxlib/enxio.c, line: 409 Fatal error: Energy names magic number mismatch, this is not a GROMACS edr file For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I would really appreciate any hint on this subject. This was a Gromacs bug in versions 4.5.1 and 4.5.2. Please upgrade to version 4.5.3. http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x -Justin Many thanks in advance. Mikhail. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] perl script for g_hbond
Olga Ivchenko wrote: Dear Justin, I ran you H bond frequency script and I got the following result. I am understanding that the occupancy of H bonds is on the writeside, but somehow in donor and acceptor column there is the residue name not atom type. I am not quiet good iunderstanding my output. Please can you advice me on this? Something is very wrong with your input. Probably your index file is incorrect. Have you read the requirements in the header of the script? You can't pass a standard hbond.ndx (output of g_hbond -hbn) to the script. It requires that the .ndx file supplied contain only the [hbonds_...] section. -Justin #DonorAcceptor % Exist. 0.040 LIG1C1 LIG1C2 0.680 LIG1H7 LIG1H9 0.040 0.040 LIG1N30.360 LIG1N20.120 LIG1O2 0.040 0.120 LIG1N1 LIG1O2 0.120 0.040 0.160 0.040 0.040 0.040 0.040 0.080 0.200 0.040 0.040 0.200 0.080 best, Olga 2010/11/29 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Olga Ivchenko wrote: Hi Leila, I am also have a task to calculate H-bonds frequency through the over all trajectory in gromacs. Please can you send me Justin's script. If he does not mind. I have several analysis scripts available to the public on my website: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html -Justin Yours sincerely, Olga 2010/11/29 leila karami karami.lei...@gmail.com mailto:karami.lei...@gmail.com mailto:karami.lei...@gmail.com mailto:karami.lei...@gmail.com Dear Mark and gromacs users thanks for your time and consideration. you said by multiplying the existence functions for hbonds between protein and water and the hbonds between water and DNA, then using Justin's script, I can obtain percentage each water medited hydrogen bond during trajectory. and also you said I need to create a corresponding index file too. I don't know where should I start for multiply two existence functions? please explain about it more. any help will highly appreciated. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users
[gmx-users] [Fwd: g_sas for each residu]
Hi all, I would like to use g_sas to compute and give surface area changes of each residu of a peptide (25 AA long) and *not* the average per residu given by the argument -or) along the simulation time. If yes how ? Of course, i think, i can use an index file, but for 25 AA, it will take a long time. Others alternatives are welcome :-) . Thank you in advance for your response Stephane -- 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] HBOND probability
Poojari, Chetan wrote: Hello Justin, I wanted to find the probability of hydrogen bond formed between my peptide and water molecules over time. So I used your plot_hbmap.pl script. As mentioned in the script file, my index file contained atom numbers only from the [hbonds...] section, rest were deleted. Heres my short output after running the script: #DonorAcceptor % Exist. 0.004 ALAA N 0.004 ALAA N 0.016 ALAA N 0.012 ALAA N 0.008 ALAA O 0.008 ASNA OD1 0.012 GLYA O 0.008 ALAA O 0.008 Please can I know if this is the expected output from the script ??? if not please can I know what might be wrong in my input This is absolutely not the correct output. Probably your index file is not correct. Also note that if you want proper residue names/numbers, you need to use a .pdb file that does not have chain identifiers. -Justin Kind regards, chetan. Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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: g_sas for each residu]
Stephane Abel wrote: Hi all, I would like to use g_sas to compute and give surface area changes of each residu of a peptide (25 AA long) and *not* the average per residu given by the argument -or) along the simulation time. If yes how ? Of course, i think, i can use an index file, but for 25 AA, it will take a long time. Others alternatives are welcome :-) . Aside from modifying the code to do this, I don't see a way that g_sas will produce what you want in a single run. -Justin Thank you in advance for your response Stephane -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] problem building Gromacs 4.5.3 using the Intel compiler
Hello, I am trying to build Gromacs 4.5.3 using the Intel compiler, but I am encountering the following problems when I type make: /bin/sh ../../libtool --tag=CC --mode=link mpicc -O3 -tpp7 -axW -ip -w -msse2 -funroll-all-loops -std=gnu99 -L/gpfs/grace/fftw-3.2.2/lib -o grompp grompp.o libgmxpreprocess_mpi_d.la ../mdlib/libmd_mpi_d.la ../gmxlib/libgmx_mpi_d.la -lnsl -lm mpicc -O3 -tpp7 -axW -ip -w -msse2 -funroll-all-loops -std=gnu99 -o grompp grompp.o -L/gpfs/grace/fftw-3.2.2/lib ./.libs/libgmxpreprocess_mpi_d.a /gpfs/ueasystem/grace/gromacs-4.5.3/src/mdlib/.libs/libmd_mpi_d.a ../mdlib/.libs/libmd_mpi_d.a /gpfs/grace/fftw-3.2.2/lib/libfftw3.a /gpfs/ueasystem/grace/gromacs-4.5.3/src/gmxlib/.libs/libgmx_mpi_d.a ../gmxlib/.libs/libgmx_mpi_d.a -lnsl -lm /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(mapflags.o): In function `timelimit_to_flags': /gpfs/ueasystem/grace/fftw-3.2.2/api/./mapflags.c:70: undefined reference to `__fmth_i_dlog' /gpfs/ueasystem/grace/fftw-3.2.2/api/./mapflags.c:70: undefined reference to `__fmth_i_dlog' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(timer.o): In function `elapsed': /gpfs/ueasystem/grace/fftw-3.2.2/kernel/./cycle.h:244: undefined reference to `__mth_i_dfloatuk' /gpfs/ueasystem/grace/fftw-3.2.2/kernel/./cycle.h:244: undefined reference to `__mth_i_dfloatuk' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(generic.o): In function `apply': /gpfs/ueasystem/grace/fftw-3.2.2/dft/./generic.c:73: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(lt8-generic.o): In function `apply_r2hc': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./generic.c:74: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(lt8-generic.o): In function `apply_hc2r': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./generic.c:128: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(vrank3-transpose.o): In function `transpose_toms513': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./vrank3-transpose.c:536: undefined reference to `__c_mzero1' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(trig.o): In function `real_cexp': /gpfs/ueasystem/grace/fftw-3.2.2/kernel/./trig.c:65: undefined reference to `__fmth_i_dsincos' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(dht-rader.o): In function `apply': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./dht-rader.c:79: undefined reference to `__c_mzero8' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(dht-rader.o): In function `mkomega': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./dht-rader.c:184: undefined reference to `__c_mzero8' /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./dht-rader.c:187: undefined reference to `__c_mcopy8_bwd' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(ct-hc2c-direct.o): In function `apply_buf': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./ct-hc2c-direct.c:130: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(dftw-direct.o): In function `apply_buf': /gpfs/ueasystem/grace/fftw-3.2.2/dft/./dftw-direct.c:103: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(direct.o): In function `apply_buf': /gpfs/ueasystem/grace/fftw-3.2.2/dft/./direct.c:74: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(direct-r2c.o): In function `iterate': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./direct-r2c.c:129: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(hc2hc-direct.o): In function `apply_buf': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./hc2hc-direct.c:96: undefined reference to `__builtin_alloca' make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/gpfs/ueasystem/grace/gromacs-4.5.3/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/gpfs/ueasystem/grace/gromacs-4.5.3/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/gpfs/ueasystem/grace/gromacs-4.5.3/src' make: *** [all-recursive] Error 1 [r...@head00 gromacs-4.5.3]# Any help will be greatly appreciated. The configure command prints the following: [r...@head00 gromacs-4.5.3]# ./configure --enable-double --enable-mpi --program-suffix=_mpi_d --prefix=/gpfs/grace/gromacs-4.5.3 checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether /gpfs/grace/intel/Compiler/11.1/073/bin/intel64/icc accepts -g... yes checking for /gpfs/grace/intel/Compiler/11.1/073/bin/intel64/icc option to accept ISO C89... none needed
Re: [gmx-users] [Fwd: g_sas for each residu]
On 12/13/10, Stephane Abel stephane.a...@cea.fr wrote: Hi all, I would like to use g_sas to compute and give surface area changes of each residu of a peptide (25 AA long) and *not* the average per residu given by the argument -or) along the simulation time. If yes how ? Of course, i think, i can use an index file, but for 25 AA, it will take a long time. Somehow you want to generate the matrix of SAS with time in one dimension and residue on the other. I forget if there's an elegant g_sas way to do this, but at worst you can trjconv separate frames, use g_sas -or, and concatenate the results into the matrix. Then IIRC tools like gnuplot will let you write a plot expression that instructs it to plot the result of subtract corresponding elements of different columns in the data set against some other value... 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] problem building Gromacs 4.5.3 using the Intel compiler
On 12/13/10, Miah Wadud Dr (ITCS) w.m...@uea.ac.uk wrote: Hello, I am trying to build Gromacs 4.5.3 using the Intel compiler, but I am encountering the following problems when I type make: It seems like there's some mismatch between how FFTW was compiled and how you're linking to it. Try a fresh FFTW compilation with this compiler, etc. Mark /bin/sh ../../libtool --tag=CC --mode=link mpicc -O3 -tpp7 -axW -ip -w -msse2 -funroll-all-loops -std=gnu99 -L/gpfs/grace/fftw-3.2.2/lib -o grompp grompp.o libgmxpreprocess_mpi_d.la ../mdlib/libmd_mpi_d.la ../gmxlib/libgmx_mpi_d.la -lnsl -lm mpicc -O3 -tpp7 -axW -ip -w -msse2 -funroll-all-loops -std=gnu99 -o grompp grompp.o -L/gpfs/grace/fftw-3.2.2/lib ./.libs/libgmxpreprocess_mpi_d.a /gpfs/ueasystem/grace/gromacs-4.5.3/src/mdlib/.libs/libmd_mpi_d.a ../mdlib/.libs/libmd_mpi_d.a /gpfs/grace/fftw-3.2.2/lib/libfftw3.a /gpfs/ueasystem/grace/gromacs-4.5.3/src/gmxlib/.libs/libgmx_mpi_d.a ../gmxlib/.libs/libgmx_mpi_d.a -lnsl -lm /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(mapflags.o): In function `timelimit_to_flags': /gpfs/ueasystem/grace/fftw-3.2.2/api/./mapflags.c:70: undefined reference to `__fmth_i_dlog' /gpfs/ueasystem/grace/fftw-3.2.2/api/./mapflags.c:70: undefined reference to `__fmth_i_dlog' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(timer.o): In function `elapsed': /gpfs/ueasystem/grace/fftw-3.2.2/kernel/./cycle.h:244: undefined reference to `__mth_i_dfloatuk' /gpfs/ueasystem/grace/fftw-3.2.2/kernel/./cycle.h:244: undefined reference to `__mth_i_dfloatuk' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(generic.o): In function `apply': /gpfs/ueasystem/grace/fftw-3.2.2/dft/./generic.c:73: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(lt8-generic.o): In function `apply_r2hc': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./generic.c:74: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(lt8-generic.o): In function `apply_hc2r': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./generic.c:128: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(vrank3-transpose.o): In function `transpose_toms513': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./vrank3-transpose.c:536: undefined reference to `__c_mzero1' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(trig.o): In function `real_cexp': /gpfs/ueasystem/grace/fftw-3.2.2/kernel/./trig.c:65: undefined reference to `__fmth_i_dsincos' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(dht-rader.o): In function `apply': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./dht-rader.c:79: undefined reference to `__c_mzero8' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(dht-rader.o): In function `mkomega': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./dht-rader.c:184: undefined reference to `__c_mzero8' /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./dht-rader.c:187: undefined reference to `__c_mcopy8_bwd' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(ct-hc2c-direct.o): In function `apply_buf': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./ct-hc2c-direct.c:130: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(dftw-direct.o): In function `apply_buf': /gpfs/ueasystem/grace/fftw-3.2.2/dft/./dftw-direct.c:103: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(direct.o): In function `apply_buf': /gpfs/ueasystem/grace/fftw-3.2.2/dft/./direct.c:74: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(direct-r2c.o): In function `iterate': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./direct-r2c.c:129: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(hc2hc-direct.o): In function `apply_buf': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./hc2hc-direct.c:96: undefined reference to `__builtin_alloca' make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/gpfs/ueasystem/grace/gromacs-4.5.3/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/gpfs/ueasystem/grace/gromacs-4.5.3/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/gpfs/ueasystem/grace/gromacs-4.5.3/src' make: *** [all-recursive] Error 1 [r...@head00 gromacs-4.5.3]# Any help will be greatly appreciated. The configure command prints the following: [r...@head00 gromacs-4.5.3]# ./configure --enable-double --enable-mpi --program-suffix=_mpi_d --prefix=/gpfs/grace/gromacs-4.5.3 checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for
Re: [gmx-users] problem building Gromacs 4.5.3 using the Intel compiler
Hi, you might also need to use the mpiicc compiler wrapper instead of the mpicc to enforce using icc instead of gcc. Carsten On Dec 13, 2010, at 2:20 PM, Mark Abraham wrote: On 12/13/10, Miah Wadud Dr (ITCS) w.m...@uea.ac.uk wrote: Hello, I am trying to build Gromacs 4.5.3 using the Intel compiler, but I am encountering the following problems when I type make: It seems like there's some mismatch between how FFTW was compiled and how you're linking to it. Try a fresh FFTW compilation with this compiler, etc. Mark /bin/sh ../../libtool --tag=CC --mode=link mpicc -O3 -tpp7 -axW -ip -w -msse2 -funroll-all-loops -std=gnu99 -L/gpfs/grace/fftw-3.2.2/lib -o grompp grompp.o libgmxpreprocess_mpi_d.la ../mdlib/libmd_mpi_d.la ../gmxlib/libgmx_mpi_d.la -lnsl -lm mpicc -O3 -tpp7 -axW -ip -w -msse2 -funroll-all-loops -std=gnu99 -o grompp grompp.o -L/gpfs/grace/fftw-3.2.2/lib ./.libs/libgmxpreprocess_mpi_d.a /gpfs/ueasystem/grace/gromacs-4.5.3/src/mdlib/.libs/libmd_mpi_d.a ../mdlib/.libs/libmd_mpi_d.a /gpfs/grace/fftw-3.2.2/lib/libfftw3.a /gpfs/ueasystem/grace/gromacs-4.5.3/src/gmxlib/.libs/libgmx_mpi_d.a ../gmxlib/.libs/libgmx_mpi_d.a -lnsl -lm /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(mapflags.o): In function `timelimit_to_flags': /gpfs/ueasystem/grace/fftw-3.2.2/api/./mapflags.c:70: undefined reference to `__fmth_i_dlog' /gpfs/ueasystem/grace/fftw-3.2.2/api/./mapflags.c:70: undefined reference to `__fmth_i_dlog' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(timer.o): In function `elapsed': /gpfs/ueasystem/grace/fftw-3.2.2/kernel/./cycle.h:244: undefined reference to `__mth_i_dfloatuk' /gpfs/ueasystem/grace/fftw-3.2.2/kernel/./cycle.h:244: undefined reference to `__mth_i_dfloatuk' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(generic.o): In function `apply': /gpfs/ueasystem/grace/fftw-3.2.2/dft/./generic.c:73: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(lt8-generic.o): In function `apply_r2hc': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./generic.c:74: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(lt8-generic.o): In function `apply_hc2r': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./generic.c:128: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(vrank3-transpose.o): In function `transpose_toms513': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./vrank3-transpose.c:536: undefined reference to `__c_mzero1' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(trig.o): In function `real_cexp': /gpfs/ueasystem/grace/fftw-3.2.2/kernel/./trig.c:65: undefined reference to `__fmth_i_dsincos' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(dht-rader.o): In function `apply': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./dht-rader.c:79: undefined reference to `__c_mzero8' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(dht-rader.o): In function `mkomega': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./dht-rader.c:184: undefined reference to `__c_mzero8' /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./dht-rader.c:187: undefined reference to `__c_mcopy8_bwd' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(ct-hc2c-direct.o): In function `apply_buf': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./ct-hc2c-direct.c:130: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(dftw-direct.o): In function `apply_buf': /gpfs/ueasystem/grace/fftw-3.2.2/dft/./dftw-direct.c:103: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(direct.o): In function `apply_buf': /gpfs/ueasystem/grace/fftw-3.2.2/dft/./direct.c:74: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(direct-r2c.o): In function `iterate': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./direct-r2c.c:129: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(hc2hc-direct.o): In function `apply_buf': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./hc2hc-direct.c:96: undefined reference to `__builtin_alloca' make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/gpfs/ueasystem/grace/gromacs-4.5.3/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/gpfs/ueasystem/grace/gromacs-4.5.3/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/gpfs/ueasystem/grace/gromacs-4.5.3/src' make: *** [all-recursive] Error 1 [r...@head00 gromacs-4.5.3]# Any help will be greatly appreciated. The configure command prints the following: [r...@head00 gromacs-4.5.3]# ./configure --enable-double --enable-mpi --program-suffix=_mpi_d --prefix=/gpfs/grace/gromacs-4.5.3 checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar
RE: [gmx-users] problem building Gromacs 4.5.3 using the Intel compiler
Hi, thanks for the advice. You were spot on: the FFTW library was compiled using PGI and Gromacs using Intel, so I have re-compiled FFTW using Intel and it all works now. Thanks ever so much people! From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Monday, December 13, 2010 1:20 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] problem building Gromacs 4.5.3 using the Intel compiler On 12/13/10, Miah Wadud Dr (ITCS) w.m...@uea.ac.uk wrote: Hello, I am trying to build Gromacs 4.5.3 using the Intel compiler, but I am encountering the following problems when I type make: It seems like there's some mismatch between how FFTW was compiled and how you're linking to it. Try a fresh FFTW compilation with this compiler, etc. Mark /bin/sh ../../libtool --tag=CC --mode=link mpicc -O3 -tpp7 -axW -ip -w -msse2 -funroll-all-loops -std=gnu99 -L/gpfs/grace/fftw-3.2.2/lib -o grompp grompp.o libgmxpreprocess_mpi_d.la ../mdlib/libmd_mpi_d.la ../gmxlib/libgmx_mpi_d.la -lnsl -lm mpicc -O3 -tpp7 -axW -ip -w -msse2 -funroll-all-loops -std=gnu99 -o grompp grompp.o -L/gpfs/grace/fftw-3.2.2/lib ./.libs/libgmxpreprocess_mpi_d.a /gpfs/ueasystem/grace/gromacs-4.5.3/src/mdlib/.libs/libmd_mpi_d.a ../mdlib/.libs/libmd_mpi_d.a /gpfs/grace/fftw-3.2.2/lib/libfftw3.a /gpfs/ueasystem/grace/gromacs-4.5.3/src/gmxlib/.libs/libgmx_mpi_d.a ../gmxlib/.libs/libgmx_mpi_d.a -lnsl -lm /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(mapflags.o): In function `timelimit_to_flags': /gpfs/ueasystem/grace/fftw-3.2.2/api/./mapflags.c:70: undefined reference to `__fmth_i_dlog' /gpfs/ueasystem/grace/fftw-3.2.2/api/./mapflags.c:70: undefined reference to `__fmth_i_dlog' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(timer.o): In function `elapsed': /gpfs/ueasystem/grace/fftw-3.2.2/kernel/./cycle.h:244: undefined reference to `__mth_i_dfloatuk' /gpfs/ueasystem/grace/fftw-3.2.2/kernel/./cycle.h:244: undefined reference to `__mth_i_dfloatuk' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(generic.o): In function `apply': /gpfs/ueasystem/grace/fftw-3.2.2/dft/./generic.c:73: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(lt8-generic.o): In function `apply_r2hc': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./generic.c:74: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(lt8-generic.o): In function `apply_hc2r': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./generic.c:128: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(vrank3-transpose.o): In function `transpose_toms513': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./vrank3-transpose.c:536: undefined reference to `__c_mzero1' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(trig.o): In function `real_cexp': /gpfs/ueasystem/grace/fftw-3.2.2/kernel/./trig.c:65: undefined reference to `__fmth_i_dsincos' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(dht-rader.o): In function `apply': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./dht-rader.c:79: undefined reference to `__c_mzero8' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(dht-rader.o): In function `mkomega': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./dht-rader.c:184: undefined reference to `__c_mzero8' /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./dht-rader.c:187: undefined reference to `__c_mcopy8_bwd' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(ct-hc2c-direct.o): In function `apply_buf': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./ct-hc2c-direct.c:130: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(dftw-direct.o): In function `apply_buf': /gpfs/ueasystem/grace/fftw-3.2.2/dft/./dftw-direct.c:103: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(direct.o): In function `apply_buf': /gpfs/ueasystem/grace/fftw-3.2.2/dft/./direct.c:74: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(direct-r2c.o): In function `iterate': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./direct-r2c.c:129: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(hc2hc-direct.o): In function `apply_buf': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./hc2hc-direct.c:96: undefined reference to `__builtin_alloca' make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/gpfs/ueasystem/grace/gromacs-4.5.3/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/gpfs/ueasystem/grace/gromacs-4.5.3/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/gpfs/ueasystem/grace/gromacs-4.5.3/src' make: *** [all-recursive] Error 1 [r...@head00 gromacs-4.5.3]# Any help will be greatly appreciated. The configure command prints the following: [r...@head00 gromacs-4.5.3]# ./configure --enable-double --enable-mpi --program-suffix=_mpi_d --prefix=/gpfs/grace/gromacs-4.5.3 checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether
[gmx-users] Question about COM-Pulling
Dear users, I've got a short question regarding com-pulling. From what I understand Umbrella pulling is the same as AFM pulling using a harmonic potential. Why is the position of the spring in the pullx.xvg not printed? One can only find the vector between both pull groups. I looked into older Gromacs manuals and in versions 4 it seems as if this data is printed to the pullx.xvg file or something similar. With kind regards, Christian -- Christian Mücksch Department of Physics TU Kaiserslautern Erwin Schrödinger Straße 67663 Kaiserslautern Germany Phone: +49 (0)631 205 4287 Fax: +49 (0)631 205 4965 Email: mueck...@rhrk.uni-kl.de -- 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] Not have PDB file of peptide
Hello Gromacs Users, If I don't have PDB file of any peptide then how can I start the simulation in Gromacs? Does Gromacs has any other way to convert peptide into Gromacs file(.gro file) ? Please help me out. -Swati -- 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] Not have PDB file of peptide
swati shah wrote: Hello Gromacs Users, If I don't have PDB file of any peptide then how can I start the simulation in Gromacs? Does Gromacs has any other way to convert peptide into Gromacs file(.gro file) ? Strictly speaking, a .gro file is not required; almost any coordinate file format will do: http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#On_the_need_for_a_.gro_file If you don't have any coordinate file whatsoever of your peptide, then you'll have to construct it: http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources -Justin Please help me out. -Swati -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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: Source code file: statutil.c, line: 727
Dear All, I am unable to carry out the md runs due to the following error. *Program grompp, VERSION 4.0.5 Source code file: statutil.c, line: 727 Invalid command line argument: * which is further followed by *Program mdrun, VERSION 4.0.5 Source code file: gmxfio.c, line: 736 Can not open file: inmd.tpr * Is the error due to parallel runs being carried out on a single machine. If so, please provide your valuable inputs to overcome this problem. yours sincerely, Uday. -- 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] ERROR: Source code file: statutil.c, line: 727
udaya kiran wrote: Dear All, I am unable to carry out the md runs due to the following error. /Program grompp, VERSION 4.0.5 Source code file: statutil.c, line: 727 Invalid command line argument: / which is further followed by /Program mdrun, VERSION 4.0.5 Source code file: gmxfio.c, line: 736 Can not open file: inmd.tpr / Is the error due to parallel runs being carried out on a single machine. If so, please provide your valuable inputs to overcome this problem. More likely the command you provided is simply wrong. Please copy and paste your mdrun command line, because it is not clear from the errors what has happened. -Justin yours sincerely, Uday. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] tpbconv extension
Dear Gromacs users, I -- 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: tpbconv extension
Dear Gromacs users, I am running a CG simulation for a peptide in lipid bilayer, and the run didnot extend after 42000 ps using gromacs 4.0.7, Reading toplogy and shit from memb12extnr42000ns.tpr Extending remaining runtime of by 1e+06 ps (now -2144967266 steps) You've simulated long enough. Not writing tpr file Please give your suggestions to overcome this error. Ram On Mon, Dec 13, 2010 at 5:26 PM, ram bio rmbio...@gmail.com wrote: Dear Gromacs users, I -- 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: tpbconv extension
ram bio wrote: Dear Gromacs users, I am running a CG simulation for a peptide in lipid bilayer, and the run didnot extend after 42000 ps using gromacs 4.0.7, Reading toplogy and shit from memb12extnr42000ns.tpr Extending remaining runtime of by 1e+06 ps (now -2144967266 steps) You've simulated long enough. Not writing tpr file Please give your suggestions to overcome this error. What was your command? -Justin Ram On Mon, Dec 13, 2010 at 5:26 PM, ram bio rmbio...@gmail.com wrote: Dear Gromacs users, I -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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: tpbconv extension
Hi Justin, The command was: tpbconv -s memb12extnr42000ns.tpr -extend 100 -o memb12extnr43000ns.tpr Thanks Ram On Mon, Dec 13, 2010 at 5:35 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs users, I am running a CG simulation for a peptide in lipid bilayer, and the run didnot extend after 42000 ps using gromacs 4.0.7, Reading toplogy and shit from memb12extnr42000ns.tpr Extending remaining runtime of by 1e+06 ps (now -2144967266 steps) You've simulated long enough. Not writing tpr file Please give your suggestions to overcome this error. What was your command? -Justin Ram On Mon, Dec 13, 2010 at 5:26 PM, ram bio rmbio...@gmail.com wrote: Dear Gromacs users, I -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-us...@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] Re: tpbconv extension
ram bio wrote: Hi Justin, The command was: tpbconv -s memb12extnr42000ns.tpr -extend 100 -o memb12extnr43000ns.tpr Try using -nsteps instead. There are issues with -extend and -until (bad rounding, limits to the size of the number, etc) that can cause this problem. I believe all of this has been resolved as of Gromacs 4.5, for future reference. -Justin Thanks Ram On Mon, Dec 13, 2010 at 5:35 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs users, I am running a CG simulation for a peptide in lipid bilayer, and the run didnot extend after 42000 ps using gromacs 4.0.7, Reading toplogy and shit from memb12extnr42000ns.tpr Extending remaining runtime of by 1e+06 ps (now -2144967266 steps) You've simulated long enough. Not writing tpr file Please give your suggestions to overcome this error. What was your command? -Justin Ram On Mon, Dec 13, 2010 at 5:26 PM, ram bio rmbio...@gmail.com wrote: Dear Gromacs users, I -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Question about COM-Pulling
The position of the reference group and the displacement of the pulled group from the reference group should be printed (although perhaps without the reference position if you are using absolute coordinate pulling, which is not recommended anyhow). If you want some better advice, please be more specific and include cut and paste sections saying I expected X at Y, but it was not in the file Z.xvg. you should also include your pull-code .mdp options and your grompp and mdrun commands. Chris. -- original message -- Dear users, I've got a short question regarding com-pulling. From what I understand Umbrella pulling is the same as AFM pulling using a harmonic potential. Why is the position of the spring in the pullx.xvg not printed? One can only find the vector between both pull groups. I looked into older Gromacs manuals and in versions 4 it seems as if this data is printed to the pullx.xvg file or something similar. With kind regards, Christian -- Christian Mücksch -- 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: tpbconv extension
Hi, No this is actually a bug in tpbconv. -nsteps will not work, because that uses a normal int, not a 64-bit integer. -dt should work, but on line 531 of src/kernel/tpbconv.c (int) should be replaced by (gmx_large_int_t). But are you sure you want to add a millisecond to your simulation time? Berk Date: Mon, 13 Dec 2010 11:40:50 -0500 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Re: tpbconv extension ram bio wrote: Hi Justin, The command was: tpbconv -s memb12extnr42000ns.tpr -extend 100 -o memb12extnr43000ns.tpr Try using -nsteps instead. There are issues with -extend and -until (bad rounding, limits to the size of the number, etc) that can cause this problem. I believe all of this has been resolved as of Gromacs 4.5, for future reference. -Justin Thanks Ram On Mon, Dec 13, 2010 at 5:35 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs users, I am running a CG simulation for a peptide in lipid bilayer, and the run didnot extend after 42000 ps using gromacs 4.0.7, Reading toplogy and shit from memb12extnr42000ns.tpr Extending remaining runtime of by 1e+06 ps (now -2144967266 steps) You've simulated long enough. Not writing tpr file Please give your suggestions to overcome this error. What was your command? -Justin Ram On Mon, Dec 13, 2010 at 5:26 PM, ram bio rmbio...@gmail.com wrote: Dear Gromacs users, I -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Re: tpbconv extension
Hi, I fixed the bug for 4.5.4. If you want an unlimited number of steps, use: tpbconv -nsteps -1 Berk From: g...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] Re: tpbconv extension Date: Mon, 13 Dec 2010 17:44:53 +0100 Hi, No this is actually a bug in tpbconv. -nsteps will not work, because that uses a normal int, not a 64-bit integer. -dt should work, but on line 531 of src/kernel/tpbconv.c (int) should be replaced by (gmx_large_int_t). But are you sure you want to add a millisecond to your simulation time? Berk Date: Mon, 13 Dec 2010 11:40:50 -0500 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Re: tpbconv extension ram bio wrote: Hi Justin, The command was: tpbconv -s memb12extnr42000ns.tpr -extend 100 -o memb12extnr43000ns.tpr Try using -nsteps instead. There are issues with -extend and -until (bad rounding, limits to the size of the number, etc) that can cause this problem. I believe all of this has been resolved as of Gromacs 4.5, for future reference. -Justin Thanks Ram On Mon, Dec 13, 2010 at 5:35 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs users, I am running a CG simulation for a peptide in lipid bilayer, and the run didnot extend after 42000 ps using gromacs 4.0.7, Reading toplogy and shit from memb12extnr42000ns.tpr Extending remaining runtime of by 1e+06 ps (now -2144967266 steps) You've simulated long enough. Not writing tpr file Please give your suggestions to overcome this error. What was your command? -Justin Ram On Mon, Dec 13, 2010 at 5:26 PM, ram bio rmbio...@gmail.com wrote: Dear Gromacs users, I -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 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: tpbconv extension
Hi Justin and Berk, Thanks for the suggestions. I am using gromacs 4.0.7 single precision, and would like to extend my run each time by 1 microsec as it fits into the wall time on the server for my system. Please suggest. Thanks Ram On Mon, Dec 13, 2010 at 5:40 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Hi Justin, The command was: tpbconv -s memb12extnr42000ns.tpr -extend 100 -o memb12extnr43000ns.tpr Try using -nsteps instead. There are issues with -extend and -until (bad rounding, limits to the size of the number, etc) that can cause this problem. I believe all of this has been resolved as of Gromacs 4.5, for future reference. -Justin Thanks Ram On Mon, Dec 13, 2010 at 5:35 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs users, I am running a CG simulation for a peptide in lipid bilayer, and the run didnot extend after 42000 ps using gromacs 4.0.7, Reading toplogy and shit from memb12extnr42000ns.tpr Extending remaining runtime of by 1e+06 ps (now -2144967266 steps) You've simulated long enough. Not writing tpr file Please give your suggestions to overcome this error. What was your command? -Justin Ram On Mon, Dec 13, 2010 at 5:26 PM, ram bio rmbio...@gmail.com wrote: Dear Gromacs users, I -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-us...@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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-us...@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] Re: tpbconv extension
Sorry, I mistook a million ps for a millisecond, this is a microsecond. The maximum number of steps in version 4.0 is INT_MAX, which is 2,147,483,647. From the name of your tpr file it seems you are not exceeding this, so I don't know what's wrong exactly. But for this reason (and many other reasons), you might want to consider upgrading to 4.5.3 (and possibly applying the bug-fix I mailed before). Berk Date: Mon, 13 Dec 2010 17:56:43 +0100 Subject: Re: [gmx-users] Re: tpbconv extension From: rmbio...@gmail.com To: jalem...@vt.edu; gmx-users@gromacs.org CC: Hi Justin and Berk, Thanks for the suggestions. I am using gromacs 4.0.7 single precision, and would like to extend my run each time by 1 microsec as it fits into the wall time on the server for my system. Please suggest. Thanks Ram On Mon, Dec 13, 2010 at 5:40 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Hi Justin, The command was: tpbconv -s memb12extnr42000ns.tpr -extend 100 -o memb12extnr43000ns.tpr Try using -nsteps instead. There are issues with -extend and -until (bad rounding, limits to the size of the number, etc) that can cause this problem. I believe all of this has been resolved as of Gromacs 4.5, for future reference. -Justin Thanks Ram On Mon, Dec 13, 2010 at 5:35 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs users, I am running a CG simulation for a peptide in lipid bilayer, and the run didnot extend after 42000 ps using gromacs 4.0.7, Reading toplogy and shit from memb12extnr42000ns.tpr Extending remaining runtime of by 1e+06 ps (now -2144967266 steps) You've simulated long enough. Not writing tpr file Please give your suggestions to overcome this error. What was your command? -Justin Ram On Mon, Dec 13, 2010 at 5:26 PM, ram bio rmbio...@gmail.com wrote: Dear Gromacs users, I -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 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] Question about COM-Pulling
Hi, this is a more general question. I thought that in analogy to an AFM-experiment a dummy-particle is placed at a certain distance from the center of mass of the pull group (compare figure 6.1 in the manual). The force is then calculated as the displacement between the pulled atom and the dummy-particle. So if this is true which I'm not sure of, I was wondering why the position of this dummy-particle is not plotted. Or does this umbrella pulling work in a different way? How is the force calculated? Thanks a lot, Christian -- The position of the reference group and the displacement of the pulled group from the reference group should be printed (although perhaps without the reference position if you are using absolute coordinate pulling, which is not recommended anyhow). If you want some better advice, please be more specific and include cut and paste sections saying I expected X at Y, but it was not in the file Z.xvg. you should also include your pull-code .mdp options and your grompp and mdrun commands. Chris. -- original message -- Dear users, I've got a short question regarding com-pulling. From what I understand Umbrella pulling is the same as AFM pulling using a harmonic potential. Why is the position of the spring in the pullx.xvg not printed? One can only find the vector between both pull groups. I looked into older Gromacs manuals and in versions 4 it seems as if this data is printed to the pullx.xvg file or something similar. With kind regards, Christian -- Christian Mücksch -- Christian Mücksch Department of Physics TU Kaiserslautern Erwin Schrödinger Straße 67663 Kaiserslautern Germany Phone: +49 (0)631 205 4287 Fax: +49 (0)631 205 4965 Email: mueck...@rhrk.uni-kl.de -- 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] HBOND probability
Hello Justin, As suggested i did remove the chain identifiers, so i do get residue numbers in my output. But the end result is still the same. While choosing 2 groups to create index file, i choose protein as my first group and sol as my second group. (I choose the entire protein and solvent group as I wanted to know the protein residues involved in hydrogen bonding with the water molecules over time) This is how my index file looks which is generated from g_hbond. (retained only hbonds) [ hbonds_Protein-SOL ] 1 2 7094 1 2 7097 1 2 7106 1 2 7112 . . 7088 7089 8 7088 7089 9 7088 7089 24 7088 7089 67 7088 7089 73 7088 7089 84 Summary.dat file contains: Donor Acceptor % Exist. 0.040 ASP1 N 0.020 ASP1 N 0.020 ASP1 N 0.100 GLU3 OE2 0.020 ARG5O 0.020 HIS6NE2 0.020 Please can i know what might be the problem here?? Kind regards, chetan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: 13 December 2010 13:37 To: Discussion list for GROMACS users Subject: Re: [gmx-users] HBOND probability Poojari, Chetan wrote: Hello Justin, I wanted to find the probability of hydrogen bond formed between my peptide and water molecules over time. So I used your plot_hbmap.pl script. As mentioned in the script file, my index file contained atom numbers only from the [hbonds...] section, rest were deleted. Heres my short output after running the script: #DonorAcceptor % Exist. 0.004 ALAA N 0.004 ALAA N 0.016 ALAA N 0.012 ALAA N 0.008 ALAA O 0.008 ASNA OD1 0.012 GLYA O 0.008 ALAA O 0.008 Please can I know if this is the expected output from the script ??? if not please can I know what might be wrong in my input This is absolutely not the correct output. Probably your index file is not correct. Also note that if you want proper residue names/numbers, you need to use a .pdb file that does not have chain identifiers. -Justin Kind regards, chetan. Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
Re: [gmx-users] Re: tpbconv extension
Hi Berk, Thanks for the suggestion, does the tpr file generated by the options mention on PC would work on a server with older version of Gromacs i.e. 4.0... Ram On Mon, Dec 13, 2010 at 6:04 PM, Berk Hess g...@hotmail.com wrote: Sorry, I mistook a million ps for a millisecond, this is a microsecond. The maximum number of steps in version 4.0 is INT_MAX, which is 2,147,483,647. From the name of your tpr file it seems you are not exceeding this, so I don't know what's wrong exactly. But for this reason (and many other reasons), you might want to consider upgrading to 4.5.3 (and possibly applying the bug-fix I mailed before). Berk Date: Mon, 13 Dec 2010 17:56:43 +0100 Subject: Re: [gmx-users] Re: tpbconv extension From: rmbio...@gmail.com To: jalem...@vt.edu; gmx-users@gromacs.org CC: Hi Justin and Berk, Thanks for the suggestions. I am using gromacs 4.0.7 single precision, and would like to extend my run each time by 1 microsec as it fits into the wall time on the server for my system. Please suggest. Thanks Ram On Mon, Dec 13, 2010 at 5:40 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Hi Justin, The command was: tpbconv -s memb12extnr42000ns.tpr -extend 100 -o memb12extnr43000ns.tpr Try using -nsteps instead. There are issues with -extend and -until (bad rounding, limits to the size of the number, etc) that can cause this problem. I believe all of this has been resolved as of Gromacs 4.5, for future reference. -Justin Thanks Ram On Mon, Dec 13, 2010 at 5:35 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs users, I am running a CG simulation for a peptide in lipid bilayer, and the run didnot extend after 42000 ps using gromacs 4.0.7, Reading toplogy and shit from memb12extnr42000ns.tpr Extending remaining runtime of by 1e+06 ps (now -2144967266 steps) You've simulated long enough. Not writing tpr file Please give your suggestions to overcome this error. What was your command? -Justin Ram On Mon, Dec 13, 2010 at 5:26 PM, ram bio rmbio...@gmail.com wrote: Dear Gromacs users, I -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-us...@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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-us...@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 list gmx-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 list gmx-us...@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] Question about COM-Pulling
Dear Christian: As per my original comments, please provide a .mdp file, sample output, and all the other things that I asked for. Chris. --original message-- this is a more general question. I thought that in analogy to an AFM-experiment a dummy-particle is placed at a certain distance from the center of mass of the pull group (compare figure 6.1 in the manual). The force is then calculated as the displacement between the pulled atom and the dummy-particle. So if this is true which I'm not sure of, I was wondering why the position of this dummy-particle is not plotted. Or does this umbrella pulling work in a different way? How is the force calculated? Thanks a lot, Christian -- The position of the reference group and the displacement of the pulled group from the reference group should be printed (although perhaps without the reference position if you are using absolute coordinate pulling, which is not recommended anyhow). If you want some better advice, please be more specific and include cut and paste sections saying I expected X at Y, but it was not in the file Z.xvg. you should also include your pull-code .mdp options and your grompp and mdrun commands. Chris. -- original message -- Dear users, I've got a short question regarding com-pulling. From what I understand Umbrella pulling is the same as AFM pulling using a harmonic potential. Why is the position of the spring in the pullx.xvg not printed? One can only find the vector between both pull groups. I looked into older Gromacs manuals and in versions 4 it seems as if this data is printed to the pullx.xvg file or something similar. With kind regards, Christian -- 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: tpbconv extension
No, the point is that in Gromacs version 4.0 (and all versions before) steps were counted in plain int's, which are 32 bit. In version 4.5 they are 64 bit. But I would suggest to upgrade to 4.5.3 for performance reasons. If you can run a microsecond, you are probably running in parallel over many core and 4.5.3 will also improve your performance. Berk Date: Mon, 13 Dec 2010 18:16:28 +0100 Subject: Re: [gmx-users] Re: tpbconv extension From: rmbio...@gmail.com To: gmx-users@gromacs.org Hi Berk, Thanks for the suggestion, does the tpr file generated by the options mention on PC would work on a server with older version of Gromacs i.e. 4.0... Ram On Mon, Dec 13, 2010 at 6:04 PM, Berk Hess g...@hotmail.com wrote: Sorry, I mistook a million ps for a millisecond, this is a microsecond. The maximum number of steps in version 4.0 is INT_MAX, which is 2,147,483,647. From the name of your tpr file it seems you are not exceeding this, so I don't know what's wrong exactly. But for this reason (and many other reasons), you might want to consider upgrading to 4.5.3 (and possibly applying the bug-fix I mailed before). Berk Date: Mon, 13 Dec 2010 17:56:43 +0100 Subject: Re: [gmx-users] Re: tpbconv extension From: rmbio...@gmail.com To: jalem...@vt.edu; gmx-users@gromacs.org CC: Hi Justin and Berk, Thanks for the suggestions. I am using gromacs 4.0.7 single precision, and would like to extend my run each time by 1 microsec as it fits into the wall time on the server for my system. Please suggest. Thanks Ram On Mon, Dec 13, 2010 at 5:40 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Hi Justin, The command was: tpbconv -s memb12extnr42000ns.tpr -extend 100 -o memb12extnr43000ns.tpr Try using -nsteps instead. There are issues with -extend and -until (bad rounding, limits to the size of the number, etc) that can cause this problem. I believe all of this has been resolved as of Gromacs 4.5, for future reference. -Justin Thanks Ram On Mon, Dec 13, 2010 at 5:35 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs users, I am running a CG simulation for a peptide in lipid bilayer, and the run didnot extend after 42000 ps using gromacs 4.0.7, Reading toplogy and shit from memb12extnr42000ns.tpr Extending remaining runtime of by 1e+06 ps (now -2144967266 steps) You've simulated long enough. Not writing tpr file Please give your suggestions to overcome this error. What was your command? -Justin Ram On Mon, Dec 13, 2010 at 5:26 PM, ram bio rmbio...@gmail.com wrote: Dear Gromacs users, I -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 list gmx-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
[gmx-users] Question about COM-Pulling
Hi, although this is not relevant to my previous question: I used mdrun like this: mdrun -v -s pull.tpr -o pull.trr -cpo pull.cpt -c pull.gro -e pull.edr -g pull.log -px pull_dist.xvg -pf pull_force.xvg With an input-file like this: ; Run-Parameter integrator = md dt = 0.002 nsteps = 100 ; OUTPUT CONTROL OPTIONS nstxout = 5000 nstvout = 5000 nstfout = 5000 nstlog = 5000 nstenergy = 5000 pull_nstxout = 100 ; pull_nstfout = 100 ; rlist = 1.2 ns_type = grid coulombtype = PME-Switch rcoulomb = 1.0 vdw-type = shift rvdw = 1.0 rvdw_switch = 0.9 pbc = xyz tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 pcoupl = Berendsen pcoupltype = isotropic tau_p = 2 ref_p = 1 compressibility = 4.5e-5 DispCorr = EnerPres continuation = yes constraint_algorithm = lincs constraints = all-bonds pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = reference pull_group1 = pull pull_rate1 = 0.01 pull_k1 = 1000 ...I get an output for pull_dist.xvg which looks sth. like this: # This file was created Fri Nov 26 16:22:53 2010 # by the following command: # /mnt/nas1/c_muecksch/GROMACS_4.5.3/bin/mdrun_mpi_4.5.3_s -v -s pull.tpr -o pull.trr -cpo pull.cpt -c pull.gro -e pull.edr -g pull.log -px pull_dist.xvg -pf pull_force.xvg # # mdrun_mpi_4.5.3_s is part of G R O M A C S: # # Grunge ROck MAChoS # @ title Pull COM @ xaxis label Time (ps) @ yaxis label Position (nm) @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend 0 Z @ s1 legend 1 dZ 0. 1.1675 3.47701 0.2000 1.1675 3.48043 0.4000 1.1675 3.4795 0.6000 1.1675 3.48214 0.8000 1.1675 3.4869 and so on In this pull_dist.xvg there is no position of a dummy-particle that is connected via a harmonic potential to the pull group (as described in Grubmüller, Helmut ; Heymann, Berthold ; Tavan, Paul: Ligand Binding: Molecular Mechanics Calculation of the Streptavidin–Biotin Rupture Force. In: Science 271 (1996)) In older version of Gromacs I believe that this was the case. Has the method changed? How is the force calculated if not by the displacment of the dummy-particle. I just wanted to know how the afm pulling in gromacs is achieved without having to look in the source-code. Thx, Christian --- Dear Christian: As per my original comments, please provide a .mdp file, sample output, and all the other things that I asked for. Chris. --original message-- this is a more general question. I thought that in analogy to an AFM-experiment a dummy-particle is placed at a certain distance from the center of mass of the pull group (compare figure 6.1 in the manual). The force is then calculated as the displacement between the pulled atom and the dummy-particle. So if this is true which I'm not sure of, I was wondering why the position of this dummy-particle is not plotted. Or does this umbrella pulling work in a different way? How is the force calculated? Thanks a lot, Christian -- The position of the reference group and the displacement of the pulled group from the reference group should be printed (although perhaps without the reference position if you are using absolute coordinate pulling, which is not recommended anyhow). If you want some better advice, please be more specific and include cut and paste sections saying I expected X at Y, but it was not in the file Z.xvg. you should also include your pull-code .mdp options and your grompp and mdrun commands. Chris. -- original message -- Dear users, I've got a short question regarding com-pulling. From what I understand Umbrella pulling is the same as AFM pulling using a harmonic potential. Why is the position of the spring in the pullx.xvg not printed? One can only find the vector between both pull groups. I looked into older Gromacs manuals and in versions 4 it seems as if this data is printed to the pullx.xvg file or something similar. With kind regards, Christian -- Christian Mücksch Department of Physics TU Kaiserslautern Erwin Schrödinger Straße 67663 Kaiserslautern Germany Phone: +49 (0)631 205 4287 Email: mueck...@rhrk.uni-kl.de -- 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: gmx-users Digest, Vol 80, Issue 88
The distance between the com of the pulled group and the dummy particle / spring you have implicit in pullf.xvg (implicit since, it's the distance modified by the force constant of the spring, to get the force). I think the best one can do (to see which are which distances and how they are related to each other), is to run a small simulation and look into the distances with a plotting program: For example if you use 'pull_geometry=position' you have: REF position of the reference group - in pullx.xvg RP distance between reference and pulled group - also in pull.xvg (this distance you can also get with g_dist and using both groups as input) PS distance between pulled group and spring - in pullf.xvg (just divide with the force constant) RS distance between reference group and spring (initial distance between spring and reference group and spring + time * pulling_velocity (modified by the pull_vector)) Since you know all three distances, you can calculated one of the with the two others and look if they are the same. So RP + PS = RS etc. With 'pull_geometry=direction' it should be similar simple, but i think with 'pull_geometry=distance' it becomes nastier, if your molecule/s start to rotate and the pulling_vector doesn't remain constant. Greetings Thomas Message: 3 Date: Mon, 13 Dec 2010 18:04:28 +0100 From: Christian M?ckschmueck...@rhrk.uni-kl.de Subject: [gmx-users] Question about COM-Pulling To: gmx-users@gromacs.org Message-ID:4d06521c.1030...@rhrk.uni-kl.de Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi, this is a more general question. I thought that in analogy to an AFM-experiment a dummy-particle is placed at a certain distance from the center of mass of the pull group (compare figure 6.1 in the manual). The force is then calculated as the displacement between the pulled atom and the dummy-particle. So if this is true which I'm not sure of, I was wondering why the position of this dummy-particle is not plotted. Or does this umbrella pulling work in a different way? How is the force calculated? Thanks a lot, Christian -- The position of the reference group and the displacement of the pulled group from the reference group should be printed (although perhaps without the reference position if you are using absolute coordinate pulling, which is not recommended anyhow). If you want some better advice, please be more specific and include cut and paste sections saying I expected X at Y, but it was not in the file Z.xvg. you should also include your pull-code .mdp options and your grompp and mdrun commands. Chris. -- original message -- Dear users, I've got a short question regarding com-pulling. From what I understand Umbrella pulling is the same as AFM pulling using a harmonic potential. Why is the position of the spring in the pullx.xvg not printed? One can only find the vector between both pull groups. I looked into older Gromacs manuals and in versions 4 it seems as if this data is printed to the pullx.xvg file or something similar. With kind regards, Christian -- 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] HBOND probability
Poojari, Chetan wrote: Hello Justin, As suggested i did remove the chain identifiers, so i do get residue numbers in my output. But the end result is still the same. While choosing 2 groups to create index file, i choose protein as my first group and sol as my second group. (I choose the entire protein and solvent group as I wanted to know the protein residues involved in hydrogen bonding with the water molecules over time) This is how my index file looks which is generated from g_hbond. (retained only hbonds) [ hbonds_Protein-SOL ] 1 2 7094 1 2 7097 1 2 7106 1 2 7112 . . 7088 7089 8 7088 7089 9 7088 7089 24 7088 7089 67 7088 7089 73 7088 7089 84 Summary.dat file contains: Donor Acceptor % Exist. 0.040 ASP1 N 0.020 ASP1 N 0.020 ASP1 N 0.100 GLU3 OE2 0.020 ARG5O 0.020 HIS6NE2 0.020 Please can i know what might be the problem here?? The script does not process hydrogen bonds involving SOL. The reason is that the atom numbering goes haywire if you have too many waters and the output doesn't make sense any more. If you need to analyze anything involving SOL, just take out the unless statement on (or around) line 151 and the closing brace a few lines later. I haven't tested that, but it should be the only thing keeping SOL from being considered. -Justin Kind regards, chetan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: 13 December 2010 13:37 To: Discussion list for GROMACS users Subject: Re: [gmx-users] HBOND probability Poojari, Chetan wrote: Hello Justin, I wanted to find the probability of hydrogen bond formed between my peptide and water molecules over time. So I used your plot_hbmap.pl script. As mentioned in the script file, my index file contained atom numbers only from the [hbonds...] section, rest were deleted. Heres my short output after running the script: #DonorAcceptor % Exist. 0.004 ALAA N 0.004 ALAA N 0.016 ALAA N 0.012 ALAA N 0.008 ALAA O 0.008 ASNA OD1 0.012 GLYA O 0.008 ALAA O 0.008 Please can I know if this is the expected output from the script ??? if not please can I know what might be wrong in my input This is absolutely not the correct output. Probably your index file is not correct. Also note that if you want proper residue names/numbers, you need to use a .pdb file that does not have chain identifiers. -Justin Kind regards, chetan. Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
Re: [gmx-users] [Fwd: g_sas for each residu]
Others alternatives are welcome. Look up NACCESS. It can do what you want on pdb frames extracted from a trajectory. --- On Mon, 12/13/10, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] [Fwd: g_sas for each residu] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, December 13, 2010, 4:45 AM Stephane Abel wrote: Hi all, I would like to use g_sas to compute and give surface area changes of each residu of a peptide (25 AA long) and *not* the average per residu given by the argument -or) along the simulation time. If yes how ? Of course, i think, i can use an index file, but for 25 AA, it will take a long time. Others alternatives are welcome :-) . Aside from modifying the code to do this, I don't see a way that g_sas will produce what you want in a single run. -Justin Thank you in advance for your response Stephane -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-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] HBOND probability
Hello Justin,
I commented out the lines from 151-161
# unless ($resn =~ /SOL/) {
# for (my $z=1; $z=$nres; $z++) {
#if ($donors{$z} == $natom) {
#$donor_names[$z] = $name;
#$donor_resn[$z] = join('', $resn, $resnum);
# } elsif ($acceptors{$z} == $natom) {
# $acceptor_names[$z] = $name;
# $acceptor_resn[$z] = join('', $resn, $resnum);
# }
# }
# }
I am ending up with the similar output.
Kind regards,
chetan.
___
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 13 December 2010 19:06
To: Gromacs Users' List
Subject: Re: [gmx-users] HBOND probability
Poojari, Chetan wrote:
Hello Justin,
As suggested i did remove the chain identifiers, so i do get residue numbers
in my output. But the end result is still the same.
While choosing 2 groups to create index file, i choose protein as my first
group and sol as my second group. (I choose the entire protein and solvent
group as I wanted to know the protein residues involved in hydrogen bonding
with the water molecules over time)
This is how my index file looks which is generated from g_hbond. (retained
only hbonds)
[ hbonds_Protein-SOL ]
1 2 7094
1 2 7097
1 2 7106
1 2 7112
.
.
7088 7089 8
7088 7089 9
7088 7089 24
7088 7089 67
7088 7089 73
7088 7089 84
Summary.dat file contains:
Donor Acceptor % Exist.
0.040
ASP1 N 0.020
ASP1 N 0.020
ASP1 N 0.100
GLU3 OE20.020
ARG5O 0.020
HIS6NE2 0.020
Please can i know what might be the problem here??
The script does not process hydrogen bonds involving SOL. The reason is that
the atom numbering goes haywire if you have too many waters and the output
doesn't make sense any more.
If you need to analyze anything involving SOL, just take out the unless
statement on (or around) line 151 and the closing brace a few lines later. I
haven't tested that, but it should be the only thing keeping SOL from being
considered.
-Justin
Kind regards,
chetan
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 13 December 2010 13:37
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] HBOND probability
Poojari, Chetan wrote:
Hello Justin,
I wanted to find the probability of hydrogen bond formed between my peptide
and water molecules over time. So I used your plot_hbmap.pl script.
As mentioned in the script file, my index file contained atom numbers only
from the [hbonds...] section, rest were deleted.
Heres my short output after running the script:
#DonorAcceptor % Exist.
0.004
ALAA N 0.004
ALAA N 0.016
ALAA N 0.012
ALAA N 0.008
ALAA O 0.008
ASNA OD1 0.012
GLYA O 0.008
ALAA O 0.008
Please can I know if this is the expected output from the script ??? if not
please can I know what might be wrong in my input
This is absolutely not the correct output. Probably your index file is not
correct. Also note that if you want proper residue names/numbers, you need to
use a .pdb file that does not have chain identifiers.
-Justin
Kind regards,
chetan.
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich
Re: [gmx-users] HBOND probability
Poojari, Chetan wrote:
Hello Justin,
I commented out the lines from 151-161
# unless ($resn =~ /SOL/) {
# for (my $z=1; $z=$nres; $z++) {
#if ($donors{$z} == $natom) {
#$donor_names[$z] = $name;
#$donor_resn[$z] = join('', $resn, $resnum);
# } elsif ($acceptors{$z} == $natom) {
# $acceptor_names[$z] = $name;
# $acceptor_resn[$z] = join('', $resn, $resnum);
# }
# }
# }
I am ending up with the similar output.
Please comment out *just* the unless line (151) and the brace that encloses it,
not the entire section. Otherwise, I suspect that nothing actually happened.
That's the entire pattern matching operation there. Without it, the script
probably doesn't do anything at all.
-Justin
Kind regards,
chetan.
___
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 13 December 2010 19:06
To: Gromacs Users' List
Subject: Re: [gmx-users] HBOND probability
Poojari, Chetan wrote:
Hello Justin,
As suggested i did remove the chain identifiers, so i do get residue numbers in
my output. But the end result is still the same.
While choosing 2 groups to create index file, i choose protein as my first
group and sol as my second group. (I choose the entire protein and solvent
group as I wanted to know the protein residues involved in hydrogen bonding
with the water molecules over time)
This is how my index file looks which is generated from g_hbond. (retained
only hbonds)
[ hbonds_Protein-SOL ]
1 2 7094
1 2 7097
1 2 7106
1 2 7112
.
.
7088 7089 8
7088 7089 9
7088 7089 24
7088 7089 67
7088 7089 73
7088 7089 84
Summary.dat file contains:
Donor Acceptor % Exist.
0.040
ASP1 N 0.020
ASP1 N 0.020
ASP1 N 0.100
GLU3 OE20.020
ARG5O 0.020
HIS6NE2 0.020
Please can i know what might be the problem here??
The script does not process hydrogen bonds involving SOL. The reason is that
the atom numbering goes haywire if you have too many waters and the output
doesn't make sense any more.
If you need to analyze anything involving SOL, just take out the unless
statement on (or around) line 151 and the closing brace a few lines later. I
haven't tested that, but it should be the only thing keeping SOL from being
considered.
-Justin
Kind regards,
chetan
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 13 December 2010 13:37
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] HBOND probability
Poojari, Chetan wrote:
Hello Justin,
I wanted to find the probability of hydrogen bond formed between my peptide and
water molecules over time. So I used your plot_hbmap.pl script.
As mentioned in the script file, my index file contained atom numbers only from
the [hbonds...] section, rest were deleted.
Heres my short output after running the script:
#DonorAcceptor % Exist.
0.004
ALAA N 0.004
ALAA N 0.016
ALAA N 0.012
ALAA N 0.008
ALAA O 0.008
ASNA OD1 0.012
GLYA O 0.008
ALAA O 0.008
Please can I know if this is the expected output from the script ??? if not
please can I know what might be wrong in my input
This is absolutely not the correct output. Probably your index file is not
correct. Also note that if you want proper residue names/numbers, you need to
use a .pdb file that does not have chain identifiers.
-Justin
Kind regards,
chetan.
Forschungszentrum Juelich GmbH
52425
[gmx-users] Re: gmx-users Digest, Vol 80, Issue 90
On 10-12-13 01:29 PM, gmx-users-requ...@gromacs.org wrote: ubject: [gmx-users] Question about COM-Pulling To: MAILINGLIST GROMACSgmx-users@gromacs.org Message-ID:4d065c09.4020...@rhrk.uni-kl.de Content-Type: text/plain; charset=UTF-8; format=flowed Hi, although this is not relevant to my previous question: It is indeed relevant. I used mdrun like this: mdrun -v -s pull.tpr -o pull.trr -cpo pull.cpt -c pull.gro -e pull.edr -g pull.log -px pull_dist.xvg -pf pull_force.xvg With an input-file like this: ; Run-Parameter integrator = md dt = 0.002 nsteps = 100 ; OUTPUT CONTROL OPTIONS nstxout = 5000 nstvout = 5000 nstfout = 5000 nstlog = 5000 nstenergy = 5000 pull_nstxout = 100 ; pull_nstfout = 100 ; rlist = 1.2 ns_type = grid coulombtype = PME-Switch rcoulomb = 1.0 vdw-type = shift rvdw = 1.0 rvdw_switch = 0.9 pbc = xyz tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 pcoupl = Berendsen pcoupltype = isotropic tau_p = 2 ref_p = 1 compressibility = 4.5e-5 DispCorr = EnerPres continuation = yes constraint_algorithm = lincs constraints = all-bonds pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = reference pull_group1 = pull pull_rate1 = 0.01 pull_k1 = 1000 ...I get an output for pull_dist.xvg which looks sth. like this: # This file was created Fri Nov 26 16:22:53 2010 # by the following command: # /mnt/nas1/c_muecksch/GROMACS_4.5.3/bin/mdrun_mpi_4.5.3_s -v -s pull.tpr -o pull.trr -cpo pull.cpt -c pull.gro -e pull.edr -g pull.log -px pull_dist.xvg -pf pull_force.xvg # # mdrun_mpi_4.5.3_s is part of G R O M A C S: # # Grunge ROck MAChoS # @ title Pull COM @ xaxis label Time (ps) @ yaxis label Position (nm) @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend 0 Z @ s1 legend 1 dZ 0. 1.1675 3.47701 0.2000 1.1675 3.48043 0.4000 1.1675 3.4795 0.6000 1.1675 3.48214 0.8000 1.1675 3.4869 and so on Here you have time, the z position of your reference group and the difference along z between your pull group and your reference group. There is no dummy particle as the spring extends between the reference group at z=1.1675 and the pull group, which in the first frame is located at z=1.1675 + 3.47701. I have used the pull code since v3.3.1 and I do not recall there ever being a dummy particle when using: pull = umbrella pull_geometry = distance It is the distance of the restraint that changes over time in your setup. Chris. In this pull_dist.xvg there is no position of a dummy-particle that is connected via a harmonic potential to the pull group (as described in Grubmüller, Helmut ; Heymann, Berthold ; Tavan, Paul: Ligand Binding: Molecular Mechanics Calculation of the Streptavidin–Biotin Rupture Force. In: Science 271 (1996)) In older version of Gromacs I believe that this was the case. Has the method changed? How is the force calculated if not by the displacment of the dummy-particle. I just wanted to know how the afm pulling in gromacs is achieved without having to look in the source-code. Thx, Christian --- Dear Christian: As per my original comments, please provide a .mdp file, sample output, and all the other things that I asked for. Chris. --original message-- this is a more general question. I thought that in analogy to an AFM-experiment a dummy-particle is placed at a certain distance from the center of mass of the pull group (compare figure 6.1 in the manual). The force is then calculated as the displacement between the pulled atom and the dummy-particle. So if this is true which I'm not sure of, I was wondering why the position of this dummy-particle is not plotted. Or does this umbrella pulling work in a different way? How is the force calculated? Thanks a lot, Christian -- The position of the reference group and the displacement of the pulled group from the reference group should be printed (although perhaps without the reference position if you are using absolute coordinate pulling, which is not recommended anyhow). If you want some better advice, please be more specific and include cut and paste sections saying I expected X at Y, but it was not in the file Z.xvg. you should also include your pull-code .mdp options and your grompp and mdrun commands. Chris. -- original message -- Dear users, I've got a short question regarding com-pulling. From what I understand Umbrella pulling is the same as AFM pulling using a harmonic potential. Why is the position of the spring in the pullx.xvg not printed? One can only find the vector between
[gmx-users] Question about COM-Pulling
Here you have time, the z position of your reference group and the difference along z between your pull group and your reference group. There is no dummy particle as the spring extends between the reference group at z=1.1675 and the pull group, which in the first frame is located at z=1.1675 + 3.47701. I have used the pull code since v3.3.1 and I do not recall there ever being a dummy particle when using: pull = umbrella pull_geometry = distance It is the distance of the restraint that changes over time in your setup. Sorry to ask again but I'm a bit confused. I thought that a spring (harmonic potential) is connected to the pull-group (by dummy-particle I meant the top of the spring=zspring) and then moved at a certain pull_rate in the desired direction. If the spring extends from the pull-group to the reference group and the reference group stays in place while the pull-group is moved away, then the spring would extend and extend and therefore the force rise and rise. What obvious fact am I missing? Is there a difference between AFM pulling and Umbrella pulling? On 10-12-13 01:29 PM,gmx-users-request at gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users wrote: / ubject: [gmx-users] Question about COM-Pulling // To: MAILINGLIST GROMACSgmx-users at gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users // Message-ID:4D065C09.4020809 at rhrk.uni-kl.de http://lists.gromacs.org/mailman/listinfo/gmx-users // Content-Type: text/plain; charset=UTF-8; format=flowed // // Hi, // // although this is not relevant to my previous question: / It is indeed relevant. / I used mdrun like this: // // mdrun -v -s pull.tpr -o pull.trr -cpo pull.cpt -c pull.gro -e pull.edr // -g pull.log -px pull_dist.xvg -pf pull_force.xvg // // With an input-file like this: // // // ; Run-Parameter // integrator = md // dt = 0.002 // nsteps = 100 // // ; OUTPUT CONTROL OPTIONS // nstxout = 5000 // nstvout = 5000 // nstfout = 5000 // nstlog = 5000 // nstenergy = 5000 // // pull_nstxout = 100 ; // pull_nstfout = 100 ; // // rlist = 1.2 // ns_type = grid // coulombtype = PME-Switch // rcoulomb = 1.0 // vdw-type = shift // rvdw = 1.0 // rvdw_switch = 0.9 // pbc = xyz // // tcoupl = V-rescale // tc-grps = Protein Non-Protein // tau_t = 0.1 0.1 // ref_t = 300 300 // // pcoupl = Berendsen // pcoupltype = isotropic // tau_p = 2 // ref_p = 1 // compressibility = 4.5e-5 // // DispCorr = EnerPres // continuation = yes // // constraint_algorithm = lincs // constraints = all-bonds // // pull = umbrella // pull_geometry = distance // pull_dim = N N Y // pull_start = yes // pull_ngroups = 1 // pull_group0 = reference // pull_group1 = pull // pull_rate1 = 0.01 // pull_k1 = 1000 // // // ...I get an output for pull_dist.xvg which looks sth. like this: // // // # This file was created Fri Nov 26 16:22:53 2010 // # by the following command: // # /mnt/nas1/c_muecksch/GROMACS_4.5.3/bin/mdrun_mpi_4.5.3_s -v -s // pull.tpr -o pull.trr -cpo pull.cpt -c pull.gro -e pull.edr -g pull.log // -px pull_dist.xvg -pf pull_force.xvg // # // # mdrun_mpi_4.5.3_s is part of G R O M A C S: // # // # Grunge ROck MAChoS // # // @ title Pull COM // @ xaxis label Time (ps) // @ yaxis label Position (nm) // @TYPE xy // @ view 0.15, 0.15, 0.75, 0.85 // @ legend on // @ legend box on // @ legend loctype view // @ legend 0.78, 0.8 // @ legend length 2 // @ s0 legend 0 Z // @ s1 legend 1 dZ // 0. 1.1675 3.47701 // 0.2000 1.1675 3.48043 // 0.4000 1.1675 3.4795 // 0.6000 1.1675 3.48214 // 0.8000 1.1675 3.4869 // // and so on / Here you have time, the z position of your reference group and the difference along z between your pull group and your reference group. There is no dummy particle as the spring extends between the reference group at z=1.1675 and the pull group, which in the first frame is located at z=1.1675 + 3.47701. I have used the pull code since v3.3.1 and I do not recall there ever being a dummy particle when using: pull = umbrella pull_geometry = distance It is the distance of the restraint that changes over time in your setup. Chris. / // // In this pull_dist.xvg there is no position of a dummy-particle that is // connected via a harmonic potential to the pull group (as described in // GrubmuÌ^ller, Helmut ; Heymann, Berthold ; Tavan, Paul: Ligand Binding: // Molecular Mechanics Calculation of the StreptavidinâEURBiotin Rupture // Force. In: Science 271 (1996)) // // In older version of Gromacs I believe that this was the case. Has the // method changed? How is the force calculated if not by the displacment of the // dummy-particle. I just wanted to know how the afm pulling in gromacs // is achieved without having
[gmx-users] mpi run in Gromacs 4.5.3
Hi, I have been trying to run Gromacs 4.5.3 parallel simulations using openmpi 1.4.2. From my understanding, mdrun_mpi is not used in this version of Gromacs. Our system administrator told me that all mpi related options have been turned on while installing Gromacs. With either commands: mdrun -np X -deffnm topol -N X (run in an 8-cpu node) or mpirun -np X mdrun -deffnm topol -N X (submitted in a number of nodes depending on availability) I get X identical simulations instead of a parallel run. If X=4, I get 4 identical simulations (the same simulation ran 4 times) instead of 1 parallel simulation in 4 processors. The performance difference between a single-processor run and the X=4 run are also similar (no marked difference in the time it takes to finish the simulation). Has anyone encountered this problem? I could provide more details if needed Thanks, JT -- 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] Question about COM-Pulling
for your setup options, the spring potential is something like: U=0.5*k*[(z_ref - z_pull) - (initial_dist + time*0.01)]^2 (please refer to the manual for more details, I don't do AFM and didn't check the exact functional form). So the spring is not on the displacement but on the difference between the actual displacement and the desired displacement, where your desired displacement is changing over time. Chris. -- original message -- Here you have time, the z position of your reference group and the difference along z between your pull group and your reference group. There is no dummy particle as the spring extends between the reference group at z=1.1675 and the pull group, which in the first frame is located at z=1.1675 + 3.47701. I have used the pull code since v3.3.1 and I do not recall there ever being a dummy particle when using: pull = umbrella pull_geometry = distance It is the distance of the restraint that changes over time in your setup. Sorry to ask again but I'm a bit confused. I thought that a spring (harmonic potential) is connected to the pull-group (by dummy-particle I meant the top of the spring=zspring) and then moved at a certain pull_rate in the desired direction. If the spring extends from the pull-group to the reference group and the reference group stays in place while the pull-group is moved away, then the spring would extend and extend and therefore the force rise and rise. What obvious fact am I missing? Is there a difference between AFM pulling and Umbrella pulling? -- snip -- -- 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] pathologically expanding box
Hello, Has anyone else experienced a pathologically expanding box during equilibration in the NPT ensemble? I've solvated my system with editconf/genbox, energy minimized, equilibrated in NVT with the protein coordinates restrained, and then equilibrated in NPT without any position restraints. During the NPT equilibration all the box dimensions are doubling and the density decreases drastically. I'm using the v-rescale thermostat and the Berendsen barostat in gromacs 4.5.3 with the AMBER03 force field and tip3p water. I've also tried OPLSAA with SPC water, a number of different box types (cubic, octahedral, dodecahedral), and shorter tau_t and tau_p settings. I also tried adding another energy minimzation step between my NVT and NPT phases. My mdp settings for the NPT ensemble are below. Thanks for your help. Greg ; RUN CONTROL PARAMETERS ;define = -DPOSRES integrator = md tinit = 0 nsteps = 5 dt = 0.002000 comm-mode = linear nstcomm = 4 ; CONSTRAINTS constraints = all-bonds lincs_order = 6 lincs_iter = 2 ; NEIGHBORSEARCHING PARAMETERS ns_type = grid nstlist = 4 rlist = 1.2 pbc = xyz ; ELECTROSTATICS coulombtype = pme ;-switch rcoulomb= 1.2 ;rcoulomb-switch = 0.80 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 0.01 ewald_geometry = 3d epsilon_surface = 0 optimize_fft= yes epsilon_r = 80 ; VDW vdw-type= switch rvdw= 1.2 rvdw-switch = 1.1 DispCorr= EnerPres ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 0 energygrps = System nstenergy = 100 nstcalcenergy = 1 nstxtcout = 0 xtc-grps= Protein Tcoupl = v-rescale tau_t = 0.5 tc-grps = System ref_t = 300 ld_seed = -1 Pcoupl = berendsen Pcoupltype = isotropic tau_p = 5 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp= 300.0 gen_seed= -1 -- 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] Question about COM-Pulling
Dear Chris, thx a lot for your help! Unfortunately, the information you provided is nowhere to be found in the manual. With best wishes, Christian -- for your setup options, the spring potential is something like: U=0.5*k*[(z_ref - z_pull) - (initial_dist + time*0.01)]^2 (please refer to the manual for more details, I don't do AFM and didn't check the exact functional form). So the spring is not on the displacement but on the difference between the actual displacement and the desired displacement, where your desired displacement is changing over time. Chris. -- original message -- / Here you have time, the z position of your reference group and the // difference along z between your pull group and your reference group. // There is no dummy particle as the spring extends between the // reference group at z=1.1675 and the pull group, which in the first // frame is located at z=1.1675 + 3.47701. // // I have used the pull code since v3.3.1 and I do not recall there ever // being a dummy particle when using: // // pull = umbrella // pull_geometry = distance // // It is the distance of the restraint that changes over time in your setup. /Sorry to ask again but I'm a bit confused. I thought that a spring (harmonic potential) is connected to the pull-group (by dummy-particle I meant the top of the spring=zspring) and then moved at a certain pull_rate in the desired direction. If the spring extends from the pull-group to the reference group and the reference group stays in place while the pull-group is moved away, then the spring would extend and extend and therefore the force rise and rise. What obvious fact am I missing? Is there a difference between AFM pulling and Umbrella pulling? -- 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] HBOND probability
Hello Justin,
I commented out line 151 and braces enclosing it.
# unless ($resn =~ /SOL/) {
for (my $z=1; $z=$nres; $z++) {
if ($donors{$z} == $natom) {
$donor_names[$z] = $name;
$donor_resn[$z] = join('', $resn, $resnum);
} elsif ($acceptors{$z} == $natom) {
$acceptor_names[$z] = $name;
$acceptor_resn[$z] = join('', $resn, $resnum);
}
}
# }
Following is the ouput:
In the beginning of the file i had these :
#DonorAcceptor % Exist.
0.040
ASP1 N 0.020
ASP1 N 0.020
ASP1 N 0.100
GLU11 OE1 0.020
GLU11 OE2 0.020
HIS13O
0.040
GLN15 OE1 0.040
Following these i had below lines., in the same file:
#DonorAcceptor % Exist.
0.040
ASP1 N SOL171 OW 0.020
ASP1 N SOL172 OW 0.020
ASP1 N SOL175 OW 0.100
ASP1 N SOL177 OW 0.020
ASP1 N SOL179 OW 0.020
.
.
.
.
SOL682 OW HIS13 O
0.020
SOL682 OW GLN15 OE1 0.020
SOL682 OW GLN15 NE2 0.040
SOL682 OW ALA21 O 0.020
SOL682 OW GLU22 OE1 0.140
Kind regards,
chetan.
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 13 December 2010 19:54
To: Gromacs Users' List
Subject: Re: [gmx-users] HBOND probability
Poojari, Chetan wrote:
Hello Justin,
I commented out the lines from 151-161
# unless ($resn =~ /SOL/) {
# for (my $z=1; $z=$nres; $z++) {
#if ($donors{$z} == $natom) {
#$donor_names[$z] = $name;
#$donor_resn[$z] = join('', $resn, $resnum);
# } elsif ($acceptors{$z} == $natom) {
# $acceptor_names[$z] = $name;
# $acceptor_resn[$z] = join('', $resn, $resnum);
# }
# }
# }
I am ending up with the similar output.
Please comment out *just* the unless line (151) and the brace that encloses it,
not the entire section. Otherwise, I suspect that nothing actually happened.
That's the entire pattern matching operation there. Without it, the script
probably doesn't do anything at all.
-Justin
Kind regards,
chetan.
___
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 13 December 2010 19:06
To: Gromacs Users' List
Subject: Re: [gmx-users] HBOND probability
Poojari, Chetan wrote:
Hello Justin,
As suggested i did remove the chain identifiers, so i do get residue numbers
in my output. But the end result is still the same.
While choosing 2 groups to create index file, i choose protein as my first
group and sol as my second group. (I choose the entire protein and solvent
group as I wanted to know the protein residues involved in hydrogen bonding
with the water molecules over time)
This is how my index file looks which is generated from g_hbond. (retained
only hbonds)
[ hbonds_Protein-SOL ]
1 2 7094
1 2 7097
1 2 7106
1 2 7112
.
.
7088 7089 8
7088 7089 9
7088 7089 24
7088 7089 67
7088 7089 73
7088 7089 84
Summary.dat file contains:
Donor Acceptor % Exist.
0.040
ASP1 N 0.020
ASP1 N 0.020
ASP1 N 0.100
GLU3 OE20.020
ARG5O 0.020
Re: [gmx-users] HBOND probability
Poojari, Chetan wrote:
Hello Justin,
I commented out line 151 and braces enclosing it.
# unless ($resn =~ /SOL/) {
for (my $z=1; $z=$nres; $z++) {
if ($donors{$z} == $natom) {
$donor_names[$z] = $name;
$donor_resn[$z] = join('', $resn, $resnum);
} elsif ($acceptors{$z} == $natom) {
$acceptor_names[$z] = $name;
$acceptor_resn[$z] = join('', $resn, $resnum);
}
}
# }
Following is the ouput:
In the beginning of the file i had these :
#DonorAcceptor % Exist.
0.040
ASP1 N 0.020
ASP1 N 0.020
ASP1 N 0.100
GLU11 OE1 0.020
GLU11 OE2 0.020
HIS13O
0.040
GLN15 OE1 0.040
Following these i had below lines., in the same file:
#DonorAcceptor % Exist.
0.040
ASP1 N SOL171 OW 0.020
ASP1 N SOL172 OW 0.020
ASP1 N SOL175 OW 0.100
ASP1 N SOL177 OW 0.020
ASP1 N SOL179 OW 0.020
.
.
.
.
SOL682 OW HIS13 O
0.020
SOL682 OW GLN15 OE1 0.020
SOL682 OW GLN15 NE2 0.040
SOL682 OW ALA21 O 0.020
SOL682 OW GLU22 OE1 0.140
Delete the original file and run the script again. The output is simply
appended if the same file is already present. Or, modify the output routines.
The latter part of the file is the expected output.
-Justin
Kind regards,
chetan.
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 13 December 2010 19:54
To: Gromacs Users' List
Subject: Re: [gmx-users] HBOND probability
Poojari, Chetan wrote:
Hello Justin,
I commented out the lines from 151-161
# unless ($resn =~ /SOL/) {
# for (my $z=1; $z=$nres; $z++) {
#if ($donors{$z} == $natom) {
#$donor_names[$z] = $name;
#$donor_resn[$z] = join('', $resn, $resnum);
# } elsif ($acceptors{$z} == $natom) {
# $acceptor_names[$z] = $name;
# $acceptor_resn[$z] = join('', $resn, $resnum);
# }
# }
# }
I am ending up with the similar output.
Please comment out *just* the unless line (151) and the brace that encloses it,
not the entire section. Otherwise, I suspect that nothing actually happened.
That's the entire pattern matching operation there. Without it, the script
probably doesn't do anything at all.
-Justin
Kind regards,
chetan.
___
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 13 December 2010 19:06
To: Gromacs Users' List
Subject: Re: [gmx-users] HBOND probability
Poojari, Chetan wrote:
Hello Justin,
As suggested i did remove the chain identifiers, so i do get residue numbers in
my output. But the end result is still the same.
While choosing 2 groups to create index file, i choose protein as my first
group and sol as my second group. (I choose the entire protein and solvent
group as I wanted to know the protein residues involved in hydrogen bonding
with the water molecules over time)
This is how my index file looks which is generated from g_hbond. (retained
only hbonds)
[ hbonds_Protein-SOL ]
1 2 7094
1 2 7097
1 2 7106
1 2 7112
.
.
7088 7089 8
7088 7089 9
7088 7089 24
7088 7089 67
7088 7089 73
7088 7089 84
Summary.dat file contains:
Donor Acceptor % Exist.
0.040
ASP1 N 0.020
ASP1 N 0.020
ASP1
[gmx-users] Re: pathologically expanding box
Hey, Greg - I believe the problem is more probably located in your GRO file or TOP file rather than in MDP one. Just visualize your structure to check if everything is OK. Also, 50 000 steps can be not enough to get the well-equilibrated configuration. What force and energy is output at the last step of your EM run? Best of luck. Dr. Vitaly V. Chaban Rochester, U.S.A. Has anyone else experienced a pathologically expanding box during equilibration in the NPT ensemble? I've solvated my system with editconf/genbox, energy minimized, equilibrated in NVT with the protein coordinates restrained, and then equilibrated in NPT without any position restraints. During the NPT equilibration all the box dimensions are doubling and the density decreases drastically. I'm using the v-rescale thermostat and the Berendsen barostat in gromacs 4.5.3 with the AMBER03 force field and tip3p water. I've also tried OPLSAA with SPC water, a number of different box types (cubic, octahedral, dodecahedral), and shorter tau_t and tau_p settings. I also tried adding another energy minimzation step between my NVT and NPT phases. -- 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] pathologically expanding box
Greg Bowman wrote: Hello, Has anyone else experienced a pathologically expanding box during equilibration in the NPT ensemble? I've solvated my system with editconf/genbox, energy minimized, equilibrated in NVT with the protein coordinates restrained, and then equilibrated in NPT without any position restraints. During the NPT equilibration all the box dimensions are doubling and the density decreases drastically. I'm using the v-rescale thermostat and the Berendsen barostat in gromacs 4.5.3 with the AMBER03 force field and tip3p water. I've also tried OPLSAA with SPC water, a number of different box types (cubic, octahedral, dodecahedral), and shorter tau_t and tau_p settings. I also tried adding another energy minimzation step between my NVT and NPT phases. Is the temperature, potential energy, etc. stable after NVT? Is the increase in box size steady, oscillating, or sudden? Does the problem persist with different combinations of thermostat and barostat, or is it limited to V-rescale + Berendsen? -Justin My mdp settings for the NPT ensemble are below. Thanks for your help. Greg ; RUN CONTROL PARAMETERS ;define = -DPOSRES integrator = md tinit = 0 nsteps = 5 dt = 0.002000 comm-mode = linear nstcomm = 4 ; CONSTRAINTS constraints = all-bonds lincs_order = 6 lincs_iter = 2 ; NEIGHBORSEARCHING PARAMETERS ns_type = grid nstlist = 4 rlist = 1.2 pbc = xyz ; ELECTROSTATICS coulombtype = pme ;-switch rcoulomb= 1.2 ;rcoulomb-switch = 0.80 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 0.01 ewald_geometry = 3d epsilon_surface = 0 optimize_fft= yes epsilon_r = 80 ; VDW vdw-type= switch rvdw= 1.2 rvdw-switch = 1.1 DispCorr= EnerPres ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 0 energygrps = System nstenergy = 100 nstcalcenergy = 1 nstxtcout = 0 xtc-grps= Protein Tcoupl = v-rescale tau_t = 0.5 tc-grps = System ref_t = 300 ld_seed = -1 Pcoupl = berendsen Pcoupltype = isotropic tau_p = 5 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp= 300.0 gen_seed= -1 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] generating new velocities and exploring more of thephase space
Thanks a lot Justin for the valuable feedback about generating different velocities a few days ago... I would like to discuss some analysis questions with the gromacs users, I tried to find solutions to the following points in the literature and/or the mailing list, unfortunately, couldn't find any.. 1- Traget: measuring the energetics of interaction (Coulomb and LJ) between certain loops within the protein structure using g_energy or g_enemate Plan: making index files with those specific loops and use the .ndx file to introduce these groups to the g_energy using the -n option as mentioned in one of the threads in the mailing list(http://lists.gromacs.org/pipermail/gmx-users/2008-December/038588.html) Problem: g_energy compiled from gormacs 4.5.2 version doesn't have an option for index files!! g_enemate has an option for groups.dat file, when I changed my loops.ndx to loops.dat and tried to use it with g_enemate, g_enemate was not able to deal with it!! Question: Is there anyway I can get the above measurment using gromacs analytical tools? 2- Traget: measuring time evolution of the size of a binding pocket along the trajectory. Approach: I was thinking that the volume of a a binding pocket between cerain loops of the studied protein can be related to the number of water molecules being able to occupy this pocket which by changing along the time trajectory can give a quantitative (yet simplified) picture about the time evolution of the volume of that pocket Question: is there anyway to measure the size (volume) of a given binding pocket using .ndx file of the surrounding loops and a specific analysis tool in Gromacs? Question: If the answer to the above question is no. Would my approach of measuring the number of the solvent molecules occupying this pocket make sense? and if yes, how can I do this using Gromacs analytical tools? I would appreciate discussing the above questions and giving any hints or answers Regards Hassan winmail.dat-- 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] generating new velocities and exploring more of thephase space
Hassan Shallal wrote: Thanks a lot Justin for the valuable feedback about generating different velocities a few days ago... I would like to discuss some analysis questions with the gromacs users, I tried to find solutions to the following points in the literature and/or the mailing list, unfortunately, couldn't find any.. 1- Traget: measuring the energetics of interaction (Coulomb and LJ) between certain loops within the protein structure using g_energy or g_enemate Plan: making index files with those specific loops and use the .ndx file to introduce these groups to the g_energy using the -n option as mentioned in one of the threads in the mailing list(http://lists.gromacs.org/pipermail/gmx-users/2008-December/038588.html) Problem: g_energy compiled from gormacs 4.5.2 version doesn't have an option for index files!! g_enemate has an option for groups.dat file, when I changed my loops.ndx to loops.dat and tried to use it with g_enemate, g_enemate was not able to deal with it!! Question: Is there anyway I can get the above measurment using gromacs analytical tools? Using special energy groups requires the use of energygrps in the .mdp file to collect the proper energy terms during the simulation. If you did not do this, you can re-run your simulation using mdrun -rerun in conjunction with a .tpr file that contains the groups you want. Otherwise, neither g_energy no g_enemat will produce anything like what you want; the decomposed energy terms simply do not exist. 2- Traget: measuring time evolution of the size of a binding pocket along the trajectory. Approach: I was thinking that the volume of a a binding pocket between cerain loops of the studied protein can be related to the number of water molecules being able to occupy this pocket which by changing along the time trajectory can give a quantitative (yet simplified) picture about the time evolution of the volume of that pocket Question: is there anyway to measure the size (volume) of a given binding pocket using .ndx file of the surrounding loops and a specific analysis tool in Gromacs? No. Question: If the answer to the above question is no. Would my approach of measuring the number of the solvent molecules occupying this pocket make sense? and if yes, how can I do this using Gromacs analytical tools? Maybe. There is no standard Gromacs tool for doing this, however. There are various other programs that may be able to handle such a task, like HOLE (http://d2o.bioch.ox.ac.uk:38080/), cavity (http://eels.kuicr.kyoto-u.ac.jp/~tnemoto/crystal/cavity/index.en.html), or g_count (http://sbcb.bioch.ox.ac.uk/oliver/software/), but having never used the first two extensively, I can't attest to their applicability. I used g_count with version 4.0.7, but I don't know if it's compatible with the 4.5 series. It may be worthwhile to look through the literature here. I'm sure there are others who have done such analysis and other programs that I didn't list here. -Justin I would appreciate discussing the above questions and giving any hints or answers Regards Hassan -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] mpi run in Gromacs 4.5.3
On 14/12/2010 7:48 AM, Te, Jerez A., Ph.D. wrote: Hi, I have been trying to run Gromacs 4.5.3 parallel simulations using openmpi 1.4.2. From my understanding, mdrun_mpi is not used in this version of Gromacs. I don't understand what (you think) you mean. You can use thread-based parallelism for processors that share common silicon, or MPI-based parallelism if a network connection is involved, but not both. The latter is named mdrun_mpi by default. Our system administrator told me that all mpi related options have been turned on while installing Gromacs. With either commands: mdrun -np X -deffnm topol -N X (run in an 8-cpu node) This won't run in parallel at all. mdrun ignores -np and -N or mpirun -np X mdrun -deffnm topol -N X (submitted in a number of nodes depending on availability) This will get you the symptoms below, but -N is still ignored. I get X identical simulations instead of a parallel run. If X=4, I get 4 identical simulations (the same simulation ran 4 times) instead of 1 parallel simulation in 4 processors. The performance difference between a single-processor run and the X=4 run are also similar (no marked difference in the time it takes to finish the simulation). Has anyone encountered this problem? You're using a serial mdrun. Use a parallel mdrun. 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] mpi run in Gromacs 4.5.3
Hi Mark, Thank you for your reply. Just to confirm, mdrun_mpi is still being used in Gromacs 4.5.3? The gromacs manual (Appendix A.5- Running Gromacs in parallel) suggested using mdrun -np 8 -s topol -v -N 8 in running a single machine with multiple (8) processors and mpirun -p goofus,doofus,fred 10 mdrun -s topol -v -N 30 to run three machines with ten processors each. You probably already know this but I am confused as to whether these commands are correct in running parallel simulations (thus the assumption that mdrun_mpi is no longer applicable in gromacs 4.5.3). So far I have not been successful in running parallel simulations (as I mentioned before the two options above would only start X identical serial processes). My bottom line is I want to run Gromacs simulation in parallel (regardless of whether it is running on one silicon with a number of processors or on different machines or nodes with a specified number of processors). I assume that in order to get mdrun_mpi, Gromacs has to be recompiled using the --enable-mpi option because currently our gromacs executable bin does not have mdrun_mpi. Our system administrator said that all mpi-related options have been enabled in compiling gromacs and still the mdrun_mpi is not found as one of the exe files. Please help. Thanks, JT -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Mark Abraham Sent: Mon 12/13/2010 4:38 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] mpi run in Gromacs 4.5.3 On 14/12/2010 7:48 AM, Te, Jerez A., Ph.D. wrote: Hi, I have been trying to run Gromacs 4.5.3 parallel simulations using openmpi 1.4.2. From my understanding, mdrun_mpi is not used in this version of Gromacs. I don't understand what (you think) you mean. You can use thread-based parallelism for processors that share common silicon, or MPI-based parallelism if a network connection is involved, but not both. The latter is named mdrun_mpi by default. Our system administrator told me that all mpi related options have been turned on while installing Gromacs. With either commands: mdrun -np X -deffnm topol -N X (run in an 8-cpu node) This won't run in parallel at all. mdrun ignores -np and -N or mpirun -np X mdrun -deffnm topol -N X (submitted in a number of nodes depending on availability) This will get you the symptoms below, but -N is still ignored. I get X identical simulations instead of a parallel run. If X=4, I get 4 identical simulations (the same simulation ran 4 times) instead of 1 parallel simulation in 4 processors. The performance difference between a single-processor run and the X=4 run are also similar (no marked difference in the time it takes to finish the simulation). Has anyone encountered this problem? You're using a serial mdrun. Use a parallel mdrun. Mark winmail.dat-- 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] mpi run in Gromacs 4.5.3
Te, Jerez A., Ph.D. wrote: Hi Mark, Thank you for your reply. Just to confirm, mdrun_mpi is still being used in Gromacs 4.5.3? The gromacs manual (Appendix A.5- Running Gromacs in parallel) suggested using mdrun -np 8 -s topol -v -N 8 in running a single machine with multiple (8) processors and mpirun -p goofus,doofus,fred 10 mdrun -s topol -v -N 30 to run three machines with ten processors each. You probably already know this but I am confused as to whether these commands are correct Those commands are outdated. I am updating the manual to fix this. in running parallel simulations (thus the assumption that mdrun_mpi is no longer applicable in gromacs 4.5.3). So far I have not been successful in running parallel simulations (as I mentioned before the two options above would only start X identical serial processes). My bottom line is I want to run Gromacs simulation in parallel (regardless of whether it is running on one silicon with a number of processors or on different machines or nodes with a specified number of processors). The exact implementation depends on the nature of your cluster setup. For instance, our aging supercomputer does not support threading, so we have to compile with --enable-mpi to produce an mdrun_mpi binary that is called via mpirun. My laptop, however, supports threading, so I can initiate a process over both cores with mdrun -nt, no external MPI support necessary. I assume that in order to get mdrun_mpi, Gromacs has to be recompiled using the --enable-mpi option because currently our gromacs executable bin does not have mdrun_mpi. Our system administrator said that all mpi-related options have been enabled in compiling gromacs and still the mdrun_mpi is not found as one of the exe files. Please help. Just because your /bin subdirectory does not have mdrun_mpi does not necessarily mean the binary was not compiled with MPI support. Based on what you have reported, it sounds like you indeed only have a serial mdrun, but it is possible to suppress the default suffix. If you have threading support, the -nt option will be printed if you issue mdrun -h. -Justin Thanks, JT -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Mark Abraham Sent: Mon 12/13/2010 4:38 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] mpi run in Gromacs 4.5.3 On 14/12/2010 7:48 AM, Te, Jerez A., Ph.D. wrote: Hi, I have been trying to run Gromacs 4.5.3 parallel simulations using openmpi 1.4.2. From my understanding, mdrun_mpi is not used in this version of Gromacs. I don't understand what (you think) you mean. You can use thread-based parallelism for processors that share common silicon, or MPI-based parallelism if a network connection is involved, but not both. The latter is named mdrun_mpi by default. Our system administrator told me that all mpi related options have been turned on while installing Gromacs. With either commands: mdrun -np X -deffnm topol -N X (run in an 8-cpu node) This won't run in parallel at all. mdrun ignores -np and -N or mpirun -np X mdrun -deffnm topol -N X (submitted in a number of nodes depending on availability) This will get you the symptoms below, but -N is still ignored. I get X identical simulations instead of a parallel run. If X=4, I get 4 identical simulations (the same simulation ran 4 times) instead of 1 parallel simulation in 4 processors. The performance difference between a single-processor run and the X=4 run are also similar (no marked difference in the time it takes to finish the simulation). Has anyone encountered this problem? You're using a serial mdrun. Use a parallel mdrun. Mark -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] mpi run in Gromacs 4.5.3
On 14/12/2010 11:14 AM, Te, Jerez A., Ph.D. wrote: Hi Mark, Thank you for your reply. Just to confirm, mdrun_mpi is still being used in Gromacs 4.5.3? The gromacs manual (Appendix A.5- Running Gromacs in parallel) suggested using mdrun -np 8 -s topol -v -N 8 in running a single machine with multiple (8) processors and mpirun -p goofus,doofus,fred 10 mdrun -s topol -v -N 30 to run three machines with ten processors each. You probably already know this but I am confused as to whether these commands are correct in running parallel simulations (thus the assumption that mdrun_mpi is no longer applicable in gromacs 4.5.3). So far I have not been successful in running parallel simulations (as I mentioned before the two options above would only start X identical serial processes). My bottom line is I want to run Gromacs simulation in parallel (regardless of whether it is running on one silicon with a number of processors or on different machines or nodes with a specified number of processors). I assume that in order to get mdrun_mpi, Gromacs has to be recompiled using the --enable-mpi option because currently our gromacs executable bin does not have mdrun_mpi. Our system administrator said that all mpi-related options have been enabled in compiling gromacs and still the mdrun_mpi is not found as one of the exe files. Please help. I echo Justin's comments. all mpi-related options seems suspicious. There's only one, --enable-mpi. Obviously you need a correctly-configured MPI compiler and environment for it to work Mark Thanks, JT -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Mark Abraham Sent: Mon 12/13/2010 4:38 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] mpi run in Gromacs 4.5.3 On 14/12/2010 7:48 AM, Te, Jerez A., Ph.D. wrote: Hi, I have been trying to run Gromacs 4.5.3 parallel simulations using openmpi 1.4.2. From my understanding, mdrun_mpi is not used in this version of Gromacs. I don't understand what (you think) you mean. You can use thread-based parallelism for processors that share common silicon, or MPI-based parallelism if a network connection is involved, but not both. The latter is named mdrun_mpi by default. Our system administrator told me that all mpi related options have been turned on while installing Gromacs. With either commands: mdrun -np X -deffnm topol -N X (run in an 8-cpu node) This won't run in parallel at all. mdrun ignores -np and -N or mpirun -np X mdrun -deffnm topol -N X (submitted in a number of nodes depending on availability) This will get you the symptoms below, but -N is still ignored. I get X identical simulations instead of a parallel run. If X=4, I get 4 identical simulations (the same simulation ran 4 times) instead of 1 parallel simulation in 4 processors. The performance difference between a single-processor run and the X=4 run are also similar (no marked difference in the time it takes to finish the simulation). Has anyone encountered this problem? You're using a serial mdrun. Use a parallel mdrun. 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
[gmx-users] md.log
Hi gmx-users: I am trying to extend my simulation run but unfortunately i deleted the file md.log. Is there any way i get my md.log file using the existing .edr or .trr files so that i can proceed further. Thank you. Rama -- 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] md.log
Ramachandran G wrote: Hi gmx-users: I am trying to extend my simulation run but unfortunately i deleted the file md.log. Is there any way i get my md.log file using the existing .edr or .trr files so that i can proceed further. No. -Justin Thank you. Rama -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Coarse-grained simulation with MARTINI
Hello I am trying to perform a CG simulation on the solvated protein but there is one question that I would like to ask for suggestion. The problem is: the volume of the periodic box varied a lot depending on the Van der Waals distance of the CG water molecule. I guess the volume variation is because of the system needs to relax to the correct density, since the number of water molecule is depending on the Van der Waals distance. Is it reasonable if I start the simulation after the volume become stable under position restraint? Thanks in advance for reading this post. -- Kuang-Yu Chang Institute of Bioinformatic and Structural Biology National Tsin Hua University 101, section 2, Kuang-Fu Road, Hsinchu 30013 Taiwan -- 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] md.log
Thank you for your help. Rama On Mon, Dec 13, 2010 at 6:39 PM, Itamar Kass itamar.k...@monash.edu wrote: Hi, the log file is not needed for extension. Use something like: grompp -f md_extension.mdp -c MD_01.gro -n system.ndx -p system.top -t MD_01.trr -r MD_01.edr -o MD_02.tpr Itamar On 14/12/10 1:29 PM, Ramachandran G wrote: Hi gmx-users: I am trying to extend my simulation run but unfortunately i deleted the file md.log. Is there any way i get my md.log file using the existing .edr or .trr files so that i can proceed further. Thank you. Rama -- In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu -- gmx-users mailing list gmx-us...@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 -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- 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] free energy calculation problem
Hi all, I am using Gromacs4.5 for free energy calculations. At the beginning 6 lambda (0, 0.2, 0.4, 0.6, 0.8, 1.0) are used to test my system. There are two problems: 1. dV/dlambda value at lambda=0.0 is more than 300,000 KJ/mol, which is ten times large than those at the other lambda values (around 30,000 KJ/mol). All simulations at each lambda value are done during 100 ps. Since all the dV/dlambda is extremely large, I am wondering what it is related to. 2. Delta G value should be similar when the conformation is transfered from B state to A and in different sign. But integrations of all dV/dlambda are both positive in both cases (A to B, and B to A) in my results. I attach free energy stuff in the input file below. ; Free energy control stuff free_energy = yes init_lambda = 0.100 foreign_lambda = 0.1 couple-lambda0 = vdw-q couple-lambda1 = vdw couple-intramol = yes nstdhdl = 10 couple-moltype = system delta_lambda = 0 sc_alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 Thanks in advance, Jin -- 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] Terminal_ARG_residue causing problem in pdb2gmx
Dear Gromacs User My pdb is homodimer with Arg as c-terminal residue. With this pdb I am etting following error in pdb2gmx command Program pdb2gmx, VERSION 4.0.7 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom OXT in residue ARG 107 not found in rtp entry with 17 atoms while sorting atoms The command executed is as follows pdb2gmx -f.pdb -o.gro -p .top I tried to change the OXT atom name in pdb file to O2, then also I am getting the same error. In .rtp entry there is ARG residue as N-ter but for C-ter ARG there is no residue. Please suggest. Waiting for helps from gromacs users. Shahid Nayem -- 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] ERROR: Source code file: statutil.c, line: 727
Dear Uday, What is the command you have given ? Please paste the command lines. sharada -- Original Message -- From: udaya kiran kiran.ud...@gmail.com To: gmx-users@gromacs.org Date: Mon, 13 Dec 2010 17:22:07 +0100 Subject: [gmx-users] ERROR: Source code file: statutil.c, line: 727 Dear All, I am unable to carry out the md runs due to the following error. Program grompp, VERSION 4.0.5 Source code file: statutil.c, line: 727 Invalid command line argument: which is further followed by Program mdrun, VERSION 4.0.5 Source code file: gmxfio.c, line: 736 Can not open file: inmd.tpr Is the error due to parallel runs being carried out on a single machine. If so, please provide your valuable inputs to overcome this problem. yours sincerely, Uday. -- gmx-users mailing list gmx-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 The person addressed in the email is the sole authorized recipient. Should you receive it in error, immediately notify the sender of the error and delete the e-mail. Any unauthorized dissemination or copying of this e-mail (or any attachment to this e-mail) or the wrongful disclosure of the information herein contained is prohibited. Also note that this form of communication is not secure, it can be intercepted, and may not necessarily be free of errors and viruses in spite of reasonable efforts to secure this medium. -- 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
