Re: [gmx-users] grompp segmentation error
Dear Justin, I am having grompp segmentation error only for the drug-enzyme complex tutorial, all other executables are ok, can this occur due to the any other reasons like following the tutorial improperly. Thanks, Ram On Tue, Jan 5, 2010 at 1:24 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks for the response. Here is the info regarding the cluster where gromacs version 4.0.5 is installed with icc compliers. $ ./configure --prefix=/usr/local/gromacs --enable-mpi --with-fft=fftw2 uname -m = x86_64 uname -r = 2.6.18-128.7.1.el5 uname -s = Linux uname -v = #1 SMP Mon Aug 24 08:21:56 EDT 2009 compilers: C and fortran Intel 10.1 Please suggest me as the grompp command also donot work with this configuration. Does grompp give any other output, or does it just seg fault? Do other executables work on this system? There are a whole host of issues that could be causing this, from 32/64 bit mismatch, shared libraries being moved, etc, so it is very difficult to diagnose. Was the whole package compiled with MPI (per the above command)? If so, there is no point, since the only MPI-enabled executable is mdrun. It may help to re-compile correctly if this is the case (a bit of a long shot, but perhaps worth trying). Do you have gcc available on the cluster, to test and see if it produces functioning code? -Justin Thanks, Ram On Mon, Jan 4, 2010 at 6:17 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks for the response. I am using gromacs 4.0.3 version on my PC and 4.0.5 on cluster, I have asked my system admin to provide the details regarding the cluster, whereas for my PC: The info is as follows: 1. The Gromacs version you are using. - 4.0.3 2. The compilers used in installing Gromacs.- gcc gcc -v Using built-in specs. Target: i386-redhat-linux Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-libgcj-multifile --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --enable-plugin --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic --host=i386-redhat-linux Thread model: posix gcc version 4.1.2 20080704 (Red Hat 4.1.2-44) The gcc 4.1.x is well-known to be buggy, and as advised on the Gromacs source code download site: WARNING: do not use the gcc 4.1.x set of compilers. They are broken. These compilers come with recent Linux distrubutions like Fedora 5/6 etc. I would suggest updating to the latest version of Gromacs (4.0.7), using a more reliable compiler (other versions of gcc, i.e. 4.0.x and older, and 4.2.x and newer, are fine). 3. Options specified during configuration. I didnot get this, can you please elaborate... Things like --enable-shared, --disable-(whatever), but I don't know that any of this is relevant. I think the compiler is the problem. -Justin 4. Specifications of your hardware. processor : 0 vendor_id : GenuineIntel cpu family : 6 model : 13 model name : Intel(R) Pentium(R) M processor 1.70GHz stepping : 6 cpu MHz : 600.000 cache size : 2048 KB fdiv_bug : no hlt_bug : no f00f_bug : no coma_bug : no fpu : yes fpu_exception : yes cpuid level : 2 wp : yes flags : fpu vme de pse tsc msr mce cx8 mtrr pge mca cmov pat clflush dts acpi mmx fxsr sse sse2 ss tm pbe up est tm2 bogomips : 1196.53 Linux version 2.6.18-8.el5 (mockbu...@builder4.centos.org) (gcc version 4.1.1 20070105 (Red Hat 4.1.1-52)) #1 SMP Thu Mar 15 19:57:35 EDT 2007 Build Operating System: Linux 2.6.18-53.1.14.el5PAE i686 Red Hat, Inc. Current Operating System: Linux localhost.localdomain 2.6.18-8.el5 #1 SMP Thu Mar 15 19:57:35 EDT 2007 i686 Build Date: 21 June 2008 Build ID: xorg-x11-server 1.1.1-48.41.el5_2.1 I would be providing the info about the cluster, once I receive it, mean please let me know if any info is missing and help me. Thanks, Ram On Thu, Dec 31, 2009 at 11:49 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs Users, Iam following Drug/Enzyme complex solvation tutorial by John E. Kerrigan, I am unable to execute the grompp step as per the tutorial, the output of grompp command is as follows: grompp -f minim.mdp -c trp_b4ion.gro -p trp.top -o trp_b4ion.tpr :-) grompp (-: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.11# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6nb.itp Opening library file
Re: [gmx-users] do_dssp
Do you have a DSSP program on your system? If no, please install executable DSSP program from http://swift.cmbi.kun.nl/gv/dssp/ website. Rasoul On Wed, Jan 6, 2010 at 11:34 AM, leila karami karami.lei...@gmail.comwrote: Hi I apply following command: do_dssp -f rrr.xtc -s .tpr -n n.ndx -map ss.map but following error is came up: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddal9qL4 ddRvmyo0 /dev/null 2 /dev/null Any help will highly appreciated! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] do_dssp
dear Rasoul I had executable dssp program, already. leila karami -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] define a new covalent bond in gromacs
How about using bond type 6 to restrain the distance without actually creating a bond between the atoms? Tom --On Tuesday, January 05, 2010 22:57:32 +0100 David van der Spoel sp...@xray.bmc.uu.se wrote: Hans HEINDL wrote: mdrun-openmm does not yet support any restraints But gromacs does. Therefore, it seems you need to patch openmm, for which you probably want to contact the openmm team. Hans Am Dienstag, den 05.01.2010, 22:12 +0100 schrieb David van der Spoel: Hans HEINDL wrote: Hi all, I need to restrain the distance of two atoms in my system (the distance is around 57 angstroms). As we plan to use mdrun-openmm which presently does not support neither distance nor position restraints we need to create a new covalent bond between the two atoms which would restrain the distance of the two atoms. (This was Peter Eastmans idea from Standford) How could we do that and where would be the best place to define (I presume the *.top file) the bond and where should the bond length and spring constant be defined? Thanks in advance Hans HEINDL University of Westminster London UK How about normal distance restraints? Have you checked the manual? -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- TJ Piggot t.pig...@bristol.ac.uk University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] define a new covalent bond in gromacs
I'll try and let you know about results Hans Am Mittwoch, den 06.01.2010, 11:15 + schrieb TJ Piggot: How about using bond type 6 to restrain the distance without actually creating a bond between the atoms? Tom --On Tuesday, January 05, 2010 22:57:32 +0100 David van der Spoel sp...@xray.bmc.uu.se wrote: Hans HEINDL wrote: mdrun-openmm does not yet support any restraints But gromacs does. Therefore, it seems you need to patch openmm, for which you probably want to contact the openmm team. Hans Am Dienstag, den 05.01.2010, 22:12 +0100 schrieb David van der Spoel: Hans HEINDL wrote: Hi all, I need to restrain the distance of two atoms in my system (the distance is around 57 angstroms). As we plan to use mdrun-openmm which presently does not support neither distance nor position restraints we need to create a new covalent bond between the two atoms which would restrain the distance of the two atoms. (This was Peter Eastmans idea from Standford) How could we do that and where would be the best place to define (I presume the *.top file) the bond and where should the bond length and spring constant be defined? Thanks in advance Hans HEINDL University of Westminster London UK How about normal distance restraints? Have you checked the manual? -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- TJ Piggot t.pig...@bristol.ac.uk University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] do_dssp
Then your executable has problem. Gromacs tool can not find DSSP for doing d_dssp. Do you put executable DSSP in the path of gromacs is installed? Rasoul. On Wed, Jan 6, 2010 at 11:58 AM, leila karami karami.lei...@gmail.comwrote: dear Rasoul I had executable dssp program, already. leila karami -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] do_dssp
On 1/6/10 5:58 AM, leila karami wrote: dear Rasoul I had executable dssp program, already. Then have you set your PATH appropriately, as well as the DSSP environment variable? See the help information for do_dssp to see the assumptions that the program is making regarding the location of the DSSP executable, as well as the numerous posts in the archive about this issue. -Justin leila karami -- 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/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/mailing_lists/users.php
Re: [gmx-users] do_dssp
On 1/6/10 6:57 AM, rasoul nasiri wrote: Then your executable has problem. Gromacs tool can not find DSSP for doing d_dssp. Do you put executable DSSP in the path of gromacs is installed? This is not necessary. One needs to set the environment variable DSSP correctly, since the default location that do_dssp expects is /usr/local/bin/dssp, not anything to do with the location of Gromacs. -Justin Rasoul. On Wed, Jan 6, 2010 at 11:58 AM, leila karami karami.lei...@gmail.com mailto:karami.lei...@gmail.com wrote: dear Rasoul I had executable dssp program, already. leila karami -- gmx-users mailing list 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/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/mailing_lists/users.php -- 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/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/mailing_lists/users.php
[gmx-users] do_dssp
dear Rasoul I put executable DSSP in /usr/local/bin and gromacs is in /usr/local/gromacs. is it true? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] do_dssp
On 1/6/10 7:05 AM, leila karami wrote: dear Rasoul I put executable DSSP in /usr/local/bin and gromacs is in /usr/local/gromacs. is it true? Is the executable named DSSP, or dssp? Case matters. DSSP is the environment variable that must be set, while dssp is the name of the executable itself. -Justin -- 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/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/mailing_lists/users.php
Re: [gmx-users] do_dssp
yes. Could you perform do_dssp properly? Rasoul On Wed, Jan 6, 2010 at 1:05 PM, leila karami karami.lei...@gmail.comwrote: dear Rasoul I put executable DSSP in /usr/local/bin and gromacs is in /usr/local/gromacs. is it true? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] do_dssp
Hi Leila! Can I add just one more note? The file dssp, that you put in the right place, has the permissions to be executed? Nuno Azoia On Wed, 2010-01-06 at 15:35 +0330, leila karami wrote: dear Rasoul I put executable DSSP in /usr/local/bin and gromacs is in /usr/local/gromacs. is it true? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Nuno Gonçalo Azoia Lopes Laboratório de Investigação em Acabamento Departamento de Engenharia Têxtil Universidade do Minho Campus de Azurém 4800-058 Guimarães Portugal Tel: +351 253 510 280 - Ext: 517 289 Fax: +351 253 510 293 Mobile: +351 965 382 487 E-mail: naz...@det.uminho.pt -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] do_dssp
Hi dear Justin The executable is dssp leila karami -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Electron Density
Hi, I want to obtain electron density for solvent in z direction for bilayer. I used following options: ] g_density -f md.xtc -s md.tpr -d z -dens electron -o electrondens.xvg -ei electrons.dat -symm -n index.ndx Atomtapes in md.gro are OH,HW1,HW2 And “electrons.dat” file contains: 3 OW= 8 HW1=1 HW2=1 But I get error: Fatal error: Invalid line in datafile at line 1 What is my error? Best wishes, Afsaneh Maleki -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Electron Density
afsaneh maleki wrote: Hi, I want to obtain electron density for solvent in z direction for bilayer. I used following options: ] g_density -f md.xtc -s md.tpr -d z -dens electron -o electrondens.xvg -ei electrons.dat -symm -n index.ndx Atomtapes in md.gro are OH,HW1,HW2 And “electrons.dat” file contains: 3 OW= 8 HW1=1 HW2=1 But I get error: Fatal error: Invalid line in datafile at line 1 What is my error? remove = sign Best wishes, Afsaneh Maleki -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] g_wham .tpr / .xvg / .dat conversion issues
Hello All, I am trying to use g_wham to view the PMF for my simulation. I read the g_wham -h help menu, and it requires .dat input files for the -if and -it input options. My output files from mdrun for -s and -pf were .tpr and .xvg files, respectively. How to I convert my .tpr and .xvg files into .dat files for use with g_wham? Thanks! -- Venk __ Venkatesh Hariharan Columbia University | Biomedical Engineering Graduate Research Assistant You must be the change you wish to see in the world. --Mohandas Karamchand Gandhi -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] g_wham .tpr / .xvg / .dat conversion issues
On 1/6/10 1:51 PM, V Hariharan wrote: Hello All, I am trying to use g_wham to view the PMF for my simulation. I read the g_wham -h help menu, and it requires .dat input files for the -if and -it input options. My output files from mdrun for -s and -pf were .tpr and .xvg files, respectively. How to I convert my .tpr and .xvg files into .dat files for use with g_wham? Thanks! From g_wham -h: * With option -it, the user provides a file which contains the filenames of the umbrella simulation run-input files (tpr files), AND, with option -ix, a file which contains filenames of the pullx mdrun output files. The tpr and pullx files must be in corresponding order, i.e. the first tpr created the first pullx, etc. The .dat files are thus ones that you must create; they are not automatically generated by mdrun or any other utility. -Justin -- Venk __ Venkatesh Hariharan Columbia University | Biomedical Engineering Graduate Research Assistant You must be the change you wish to see in the world. --Mohandas Karamchand Gandhi -- 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/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/mailing_lists/users.php
Re: [gmx-users] do_dssp
On 1/6/10 7:52 AM, leila karami wrote: Hi dear Justin The executable is dssp leila karami Do you have the correct mode set for the executable (i.e., is it actually executable)? Did you use a pre-compiled binary, or compile it yourself from source? If you issue which dssp does your shell find the executable (again going back to potential PATH or environment issues)? -Justin -- 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/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/mailing_lists/users.php
[gmx-users] Added Residue Name [ HFL ] in ffgmx.rtp, still have err message says
Fatal error: Residue 'HFL' not found in residue topology database the portion of ffgmax.rtp file relevant is: . [ HFL ] [ atoms ] HHF HHF 0.725 0 FHF FHF 0.725 0 [ HIS1 ] ... Atom types HHF and FHF are also defined in relevant .atp file. and a simple HF.pdb file is : ATOM 1 HHF HFL 1 0.000 0.000 0.000 1.00 0.00 ATOM 2 FHF HFL 1 0.091 0.000 0.000 1.00 0.00 ATOM 3 HHF HFL 2 0.291 0.000 0.000 1.00 0.00 ATOM 4 FHF HFL 2 0.291 0.091 0.000 1.00 0.00 after issue command pdb2gmx -f HF.pdb, the following output is produced: ...Opening library file /home/fxu/gromacs/share/gromacs/top/ffgmx.rtp Opening library file /home/fxu/gromacs/share/gromacs/top/aminoacids.dat Opening library file /home/fxu/gromacs/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /home/fxu/gromacs/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /home/fxu/gromacs/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /home/fxu/gromacs/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /home/fxu/gromacs/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /home/fxu/gromacs/share/gromacs/top/elements.dat Entries in elements.dat: 218 Reading HF.pdb... Read 'Liquid HydroFloride - Yummie!', 4 atoms Opening library file /home/fxu/gromacs/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 2 residues with 4 atoms chain #res #atoms 1 ' ' 2 4 All occupancies are one Opening library file /home/fxu/gromacs/share/gromacs/top/ffgmx.atp Atomtype 1 Reading residue database... (ffgmx) Opening library file /home/fxu/gromacs/share/gromacs/top/ffgmx.rtp Residue 98 Sorting it all out... Opening library file /home/fxu/gromacs/share/gromacs/top/ffgmx.hdb Opening library file /home/fxu/gromacs/share/gromacs/top/ffgmx-n.tdb Opening library file /home/fxu/gromacs/share/gromacs/top/ffgmx-c.tdb Back Off! I just backed up topol.top to ./#topol.top.11# Processing chain 1 (4 atoms, 2 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds --- Program pdb2gmx, VERSION 4.0.7 Source code file: resall.c, line: 426 Fatal error: Residue 'HFL' not found in residue topology database --- If You See Me Getting High, Knock Me Down (Red Hot Chili Peppers) What is wrong here? Thanks, Feng Xu Postdoc @ Iowa State University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Added Residue Name [ HFL ] in ffgmx.rtp, still have err message says
On 1/6/10 5:05 PM, Feng Xu wrote: Fatal error: Residue'HFL' not found in residue topology database the portion of ffgmax.rtp file relevant is: If you have a file called ffgmax.rtp, then none of the changes you made are going to be applied, since pdb2gmx is expecting ffgmx* files. The reason I say this is because your example works quite perfectly for me using the .rtp entry and .pdb file you've posted. . [ HFL ] [ atoms ] HHF HHF 0.725 0 FHF FHF 0.725 0 Some unsolicited advice: surely you want a negative charge on the fluorine, and a bond between these two atoms, correct? [ HIS1 ] ... Atom types HHF and FHF are also defined in relevant .atp file. and a simple HF.pdb file is : ATOM 1 HHF HFL 1 0.000 0.000 0.000 1.00 0.00 ATOM 2 FHF HFL 1 0.091 0.000 0.000 1.00 0.00 ATOM 3 HHF HFL 2 0.291 0.000 0.000 1.00 0.00 ATOM 4 FHF HFL 2 0.291 0.091 0.000 1.00 0.00 Maybe there is an issue with spacing? PDB format is fixed, and the spacing between your atom names and residue names is not correct on all lines (assuming this is not just some weird behavior of my email client, but it does appear incorrect using a fixed-format font. -Justin after issue commandpdb2gmx -f HF.pdb, the following output is produced: ...Opening library file /home/fxu/gromacs/share/gromacs/top/ffgmx.rtp Opening library file /home/fxu/gromacs/share/gromacs/top/aminoacids.dat Opening library file /home/fxu/gromacs/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /home/fxu/gromacs/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /home/fxu/gromacs/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /home/fxu/gromacs/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /home/fxu/gromacs/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /home/fxu/gromacs/share/gromacs/top/elements.dat Entries in elements.dat: 218 Reading HF.pdb... Read'Liquid HydroFloride - Yummie!', 4 atoms Opening library file /home/fxu/gromacs/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 2 residues with 4 atoms chain #res #atoms 1' ' 2 4 All occupancies are one Opening library file /home/fxu/gromacs/share/gromacs/top/ffgmx.atp Atomtype 1 Reading residue database... (ffgmx) Opening library file /home/fxu/gromacs/share/gromacs/top/ffgmx.rtp Residue 98 Sorting it all out... Opening library file /home/fxu/gromacs/share/gromacs/top/ffgmx.hdb Opening library file /home/fxu/gromacs/share/gromacs/top/ffgmx-n.tdb Opening library file /home/fxu/gromacs/share/gromacs/top/ffgmx-c.tdb Back Off! I just backed up topol.top to ./#topol.top.11# Processing chain 1 (4 atoms, 2 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds --- Program pdb2gmx, VERSION 4.0.7 Source code file: resall.c, line: 426 Fatal error: Residue'HFL' not found in residue topology database --- If You See Me Getting High, Knock Me Down (Red Hot Chili Peppers) What is wrong here? Thanks, Feng Xu Postdoc @ Iowa State University -- 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/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/mailing_lists/users.php
[gmx-users] FWD:simulationg a distance restraint with a type 6 bond in gromacs
Please keep all correspondence on the GROMACS mailing list, it gives you a much greater chance of someone being able to help you. I have used this bond type before and have had no problems (with force constants much smaller than those which you apply). I would make sure that your box is big enough so that this bond is not being applied across the boundary. Otherwise someone else may have more ideas to help you. Tom Forwarded Message Date: Wednesday, January 06, 2010 22:43:20 +0100 From: Hans HEINDL hhei...@terra.es To: TJ Piggot t.pig...@bristol.ac.uk Cc: Subject: simulationg a distance restraint with a type 6 bond in gromacs Hi, As you remember we discussed simulation of a restraint which is not yet implemented in mdrun-openmm by creating a 'bond'. Type 1 bonds did not work but the type 6 did the job but I could not restrain the distance at the value I projected. The distance between the ends of my peptide should remain 57 angstroms and the best I accomplished was holding the distance fairly well for a ns and then it broke down to a much smaller value. (I tried to define the bond with: 1 614 65.761 40 with the energy term for the bond length obviously too small. But even if I got up to 300 000 000 up to 1 000 000 000 I got no proper result. The best results were recieved with 1 614 5 5.671 5.671 5.671 5.671 but even with such an extreme example the distance tended to shrink kind regards Hans HEINDL University of Westminster UK -- End Forwarded Message -- -- TJ Piggot t.pig...@bristol.ac.uk University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] FWD:simulationg a distance restraint with a type 6 bond in gromacs
Thanks Tom, It may easily be that the 6- bond type works in mdrun but not in mdrun-openmm. This would be an explanation for the ridiculous force constants Hans Am Mittwoch, den 06.01.2010, 23:15 + schrieb TJ Piggot: Please keep all correspondence on the GROMACS mailing list, it gives you a much greater chance of someone being able to help you. I have used this bond type before and have had no problems (with force constants much smaller than those which you apply). I would make sure that your box is big enough so that this bond is not being applied across the boundary. Otherwise someone else may have more ideas to help you. Tom Forwarded Message Date: Wednesday, January 06, 2010 22:43:20 +0100 From: Hans HEINDL hhei...@terra.es To: TJ Piggot t.pig...@bristol.ac.uk Cc: Subject: simulationg a distance restraint with a type 6 bond in gromacs Hi, As you remember we discussed simulation of a restraint which is not yet implemented in mdrun-openmm by creating a 'bond'. Type 1 bonds did not work but the type 6 did the job but I could not restrain the distance at the value I projected. The distance between the ends of my peptide should remain 57 angstroms and the best I accomplished was holding the distance fairly well for a ns and then it broke down to a much smaller value. (I tried to define the bond with: 1 614 65.761 40 with the energy term for the bond length obviously too small. But even if I got up to 300 000 000 up to 1 000 000 000 I got no proper result. The best results were recieved with 1 614 5 5.671 5.671 5.671 5.671 but even with such an extreme example the distance tended to shrink kind regards Hans HEINDL University of Westminster UK -- End Forwarded Message -- -- TJ Piggot t.pig...@bristol.ac.uk University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Energy units
Hi all, This may be a silly and trivial question, but the energy unit given in Gromacs is kJ/mol. What I don't quite understand is, the energy is per mole of what exactly? The energy is system size dependent, so if I double the number of molecules, the energy will double accordingly. But then the unit kJ/mol seems to imply that it is size-independent. So how do I reconcile this? Also, let's say I have a protein molecule surrounded by water molecules. Again in this case, I don't quite understand what per mole means in this case. Thanks in advance for any insights you can teach me. Daniel This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Electron Density2
Dear David van der Spoel, Would you please elaborate on the details? I didn’t underestand about “remove = sign” thanks in advans, Afsaneh Maleki -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Electron Density2
afsaneh maleki wrote: Dear David van der Spoel, Would you please elaborate on the details? I didn’t underestand about “remove = sign” Please include the previous email in your follow-up. You may only be asking one question, so that you remember your context, but any reader almost certainly doesn't. David's statement is likely to be literally true. You have an equality symbol somewhere where it should not be. 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/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/mailing_lists/users.php
[gmx-users] simulation broke at 4.0.5 version
Hi I am using Gromacs version 4.0.5. I put one protein in a simulation box with water molecules and CL- only. My simulation broke at the step, Relaxation of solvent and hydrogen atom position. Here are the .top file, command, output of the grommp, pr.mdp. anything wrong here? Thank you Lin *[6YZ.top]* [ molecules ] ; Compound#mols Protein_A 1 SOL 6504 CL- 8 *Relaxation of solvent and hydrogen atom positions: Position restrained MD* *[command]* grompp_mpi -v -f pr.mdp -c 6LYZ-EM-solvated.gro -p 6LYZ.top -o 6LYZ-PR.tpr mpiexec -np 16 mdrun_mpi -deffnm 6LYZ-PR *[output of the grompp comand]* grompp_mpi -v -f pr.mdp -c 6LYZ-EM-solvated.gro -p 6LYZ.top -o 6LYZ-PR.tpr :-) G R O M A C S (-: Gyas ROwers Mature At Cryogenic Speed :-) VERSION 4.0.5 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp_mpi (-: Option Filename Type Description -f pr.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c 6LYZ-EM-solvated.gro InputStructure file: gro g96 pdb tpr tpb tpa -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -n index.ndx Input, Opt. Index file -p 6LYZ.top InputTopology file -pp processed.top Output, Opt. Topology file -o6LYZ-PR.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -niceint0 Set the nicelevel -[no]v bool yes Be loud and noisy -timereal -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int0 Number of allowed warnings during input processing -[no]zerobool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Ignoring obsolete mdp entry 'cpp' Replacing old mdp entry 'unconstrained-start' by 'continuation' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... NOTE 1 [file pr.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. processing topology... Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG45a3.itp Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG45a3nb.itp Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG45a3bon.itp Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ff_dum.itp Generated 141 of the 1176 non-bonded parameter combinations Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'CL-' turning all bonds into constraints... processing coordinates... double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 200 K Reading position restraint coords from 6LYZ-EM-solvated.gro renumbering atomtypes... converting bonded parameters... initialising group options... processing index file... Analysing residue names: Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/aminoacids.dat There are: 6512 OTHER residues There are: 129PROTEIN residues There are: 0DNA residues Analysing Protein... Analysing Other... Making dummy/rest group for Acceleration containing 20841 elements Making dummy/rest group for Freeze containing 20841 elements Making dummy/rest group for VCM containing 20841 elements Number of degrees of
[gmx-users] Electron Density3
Hi , I want to obtain electron density for solvent in z direction for bilayer. I used following options: ] g_density -f md.xtc -s md.tpr -d z -dens electron -o electrondens.xvg -ei electrons.dat -symm -n index.ndx Atomtapes in md.gro are OH,HW1,HW2 And “electrons.dat” file contains: 3 OW= 8 HW1=1 HW2=1 But I get error: Fatal error: Invalid line in datafile at line 1 What is my error? Would you please elaborate on the details? thanks in advance very much, Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Energy units
Cheong Wee Loong, Daniel wrote: Hi all, This may be a silly and trivial question, but the energy unit given in Gromacs is kJ/mol. What I don’t quite understand is, the energy is per mole of what exactly? In a very real sense, it doesn't matter. It's just a label for a convenient bucket of energy for chemistry. The energy of an isolated water molecule has a certain value, which we might measure in joules relative to some defined zero. Two such molecules at infinite separation would have twice that energy, etc. Once we start approaching Avogadro's number, we would prefer to express that energy as kJ/mol just for our numerical convenience. Equally, we could take a water molecule and a methane molecule at infinite separation, and add their energy... and add lots more... and get irritated at the size of the number, and just divide by Avogadro for convenience. The system is no longer homogeneous, but so long as we compare energies formed in the same way, our conclusions will be valid. MD force fields are typically parameterized against things like experimental or computational enthalpies of formation, normally measured in kJ/mol (unless you're a unlucky enough to be American!). So the parameters that get derived are conveniently measured in units derived from kJ/mol. We could convert them to absolute joules, but the numbers would all be stupid. There's a reason quantum chemists work in Hartrees! Were we to work in absolute joules, the numbers we'd produce then would still relate to the numbers we actually produce in kJ/mol - by Avogadro. Mark The energy is system size dependent, so if I double the number of molecules, the energy will double accordingly. But then the unit kJ/mol seems to imply that it is size-independent. So how do I reconcile this? Also, let’s say I have a protein molecule surrounded by water molecules. Again in this case, I don’t quite understand what “per mole” means in this case. Thanks in advance for any insights you can teach me. Daniel This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Electron Density3
afsaneh maleki wrote: Hi , I want to obtain electron density for solvent in z direction for bilayer. I used following options: ] g_density -f md.xtc -s md.tpr -d z -dens electron -o electrondens.xvg -ei electrons.dat -symm -n index.ndx Atomtapes in md.gro are OH,HW1,HW2 And “electrons.dat” file contains: 3 OW= 8 HW1=1 HW2=1 But I get error: Fatal error: Invalid line in datafile at line 1 What is my error? Would you please elaborate on the details? Unfortunately this GROMACS tool seems to date from the bad old days when it was common practice for computational tools to be sensitive to whitespace in input. The code requires = as the separator, not =. 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/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/mailing_lists/users.php
Re: [gmx-users] simulation broke at 4.0.5 version
Chih-Ying Lin wrote: Hi I am using Gromacs version 4.0.5. I put one protein in a simulation box with water molecules and CL- only. My simulation broke at the step, Relaxation of solvent and hydrogen atom position. Here are the .top file, command, output of the grommp, pr.mdp. anything wrong here? Not obviously. Depending what you mean by broke, your starting configuration is probably broken, or you've mismatched input files in some way. Mark Thank you Lin *[6YZ.top]* [ molecules ] ; Compound#mols Protein_A 1 SOL 6504 CL- 8 *Relaxation of solvent and hydrogen atom positions: Position restrained MD* *[command]* grompp_mpi -v -f pr.mdp -c 6LYZ-EM-solvated.gro -p 6LYZ.top -o 6LYZ-PR.tpr mpiexec -np 16 mdrun_mpi -deffnm 6LYZ-PR *[output of the grompp comand]* grompp_mpi -v -f pr.mdp -c 6LYZ-EM-solvated.gro -p 6LYZ.top -o 6LYZ-PR.tpr :-) G R O M A C S (-: Gyas ROwers Mature At Cryogenic Speed :-) VERSION 4.0.5 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org http://www.gromacs.org/ for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp_mpi (-: Option Filename Type Description -f pr.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c 6LYZ-EM-solvated.gro InputStructure file: gro g96 pdb tpr tpb tpa -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -n index.ndx Input, Opt. Index file -p 6LYZ.top InputTopology file -pp processed.top Output, Opt. Topology file -o6LYZ-PR.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -niceint0 Set the nicelevel -[no]v bool yes Be loud and noisy -timereal -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int0 Number of allowed warnings during input processing -[no]zerobool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Ignoring obsolete mdp entry 'cpp' Replacing old mdp entry 'unconstrained-start' by 'continuation' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... NOTE 1 [file pr.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. processing topology... Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG45a3.itp Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG45a3nb.itp Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG45a3bon.itp Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ff_dum.itp Generated 141 of the 1176 non-bonded parameter combinations Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'CL-' turning all bonds into constraints... processing coordinates... double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 200 K Reading position restraint coords from 6LYZ-EM-solvated.gro renumbering atomtypes... converting bonded parameters... initialising group options... processing index file... Analysing residue names: Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/aminoacids.dat There are: 6512 OTHER residues There are: 129PROTEIN residues There are: 0DNA residues Analysing
RE: [gmx-users] Energy units
Thanks Mark for your reply. So if I understand you correctly, it's not really a mole of anything in particular, it's just an energy value divided by Avogadro's number, and this happens to be consistent with the forcefield parameters as well. So if you have just a single molecule, that energy value is still divided by Avogadro's number. So if I were to take an interaction energy per unit area to estimate an interfacial energy, and I want to relate this to an experimental value given in dynes/cm, I would just need to multiply by Avogadro's number, in addition to all the other unit conversions (kJ/nm2 to dynes/cm), for the units to be consistent. Am I correct in my understanding? Daniel -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Thursday, January 07, 2010 3:03 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy units Cheong Wee Loong, Daniel wrote: Hi all, This may be a silly and trivial question, but the energy unit given in Gromacs is kJ/mol. What I don't quite understand is, the energy is per mole of what exactly? In a very real sense, it doesn't matter. It's just a label for a convenient bucket of energy for chemistry. The energy of an isolated water molecule has a certain value, which we might measure in joules relative to some defined zero. Two such molecules at infinite separation would have twice that energy, etc. Once we start approaching Avogadro's number, we would prefer to express that energy as kJ/mol just for our numerical convenience. Equally, we could take a water molecule and a methane molecule at infinite separation, and add their energy... and add lots more... and get irritated at the size of the number, and just divide by Avogadro for convenience. The system is no longer homogeneous, but so long as we compare energies formed in the same way, our conclusions will be valid. MD force fields are typically parameterized against things like experimental or computational enthalpies of formation, normally measured in kJ/mol (unless you're a unlucky enough to be American!). So the parameters that get derived are conveniently measured in units derived from kJ/mol. We could convert them to absolute joules, but the numbers would all be stupid. There's a reason quantum chemists work in Hartrees! Were we to work in absolute joules, the numbers we'd produce then would still relate to the numbers we actually produce in kJ/mol - by Avogadro. Mark The energy is system size dependent, so if I double the number of molecules, the energy will double accordingly. But then the unit kJ/mol seems to imply that it is size-independent. So how do I reconcile this? Also, let's say I have a protein molecule surrounded by water molecules. Again in this case, I don't quite understand what per mole means in this case. Thanks in advance for any insights you can teach me. Daniel This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Energy units
Cheong Wee Loong, Daniel wrote: Thanks Mark for your reply. So if I understand you correctly, it's not really a mole of anything in particular, it's just an energy value divided by Avogadro's number, and this happens to be consistent with the forcefield parameters as well. So if you have just a single molecule, that energy value is still divided by Avogadro's number. So if I were to take an interaction energy per unit area to estimate an interfacial energy, and I want to relate this to an experimental value given in dynes/cm, I would just need to multiply by Avogadro's number, in addition to all the other unit conversions (kJ/nm2 to dynes/cm), for the units to be consistent. Am I correct in my understanding? I think so. Whether such a quantity can be measured with an MM force field might be another matter! Mark -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Thursday, January 07, 2010 3:03 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy units Cheong Wee Loong, Daniel wrote: Hi all, This may be a silly and trivial question, but the energy unit given in Gromacs is kJ/mol. What I don't quite understand is, the energy is per mole of what exactly? In a very real sense, it doesn't matter. It's just a label for a convenient bucket of energy for chemistry. The energy of an isolated water molecule has a certain value, which we might measure in joules relative to some defined zero. Two such molecules at infinite separation would have twice that energy, etc. Once we start approaching Avogadro's number, we would prefer to express that energy as kJ/mol just for our numerical convenience. Equally, we could take a water molecule and a methane molecule at infinite separation, and add their energy... and add lots more... and get irritated at the size of the number, and just divide by Avogadro for convenience. The system is no longer homogeneous, but so long as we compare energies formed in the same way, our conclusions will be valid. MD force fields are typically parameterized against things like experimental or computational enthalpies of formation, normally measured in kJ/mol (unless you're a unlucky enough to be American!). So the parameters that get derived are conveniently measured in units derived from kJ/mol. We could convert them to absolute joules, but the numbers would all be stupid. There's a reason quantum chemists work in Hartrees! Were we to work in absolute joules, the numbers we'd produce then would still relate to the numbers we actually produce in kJ/mol - by Avogadro. Mark The energy is system size dependent, so if I double the number of molecules, the energy will double accordingly. But then the unit kJ/mol seems to imply that it is size-independent. So how do I reconcile this? Also, let's say I have a protein molecule surrounded by water molecules. Again in this case, I don't quite understand what per mole means in this case. Thanks in advance for any insights you can teach me. Daniel This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
