Re: [gmx-users] problem in loading xtc in VMD
For VMD you first load a GRO (or pdb) file, and then XTC. The XTC file should contain _exactly_ the same number of atoms as the GRO file. Did you save the entire system in the XTC, or just a specific part of it? Omer. Koby Levy research group, Weizmann Institute of Science. FAX: 972-77-444-7905 http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Fri, Oct 2, 2009 at 20:39, Paymon Pirzadeh ppirz...@ucalgary.ca wrote: Hello, I ran an NVT simulation from a minimized configuration. The simulation ended normally and I have a final configuration as well. But, when I load the initial coordinates and then I want to add data, which is the xtc file, nothing happens! no frames are loaded. This is while the xtc file has a reasonable size and when I load it individually in VMD, it loads the exact number of frames it should (300 frames). Is something wrong with my outputs or is there something with VMD. This is the second system I have such a problem. Regards, Payman ___ 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] option for finding forces between two groups
Work with groups and an index file, and define energy_groups in the mdp file also. For indices, check make_ndx utility. Omer. Koby Levy research group, Weizmann Institute of Science. FAX: 972-77-444-7905 http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Fri, Oct 2, 2009 at 20:31, Pradip Biswas biswas...@gmail.com wrote: Hi, Anyone can please tell me whether there is any option in GROMACS to find forces between two groups (say for example, between two residues in a protein or between a peptide and a residue in a Protein for Protein-peptide interaction) or one need to workaround with the code to get that? Thanks in advance. Biswas. ___ 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] R.E.D.-III.3 tools release - q4md-forcefieldtools.org
Dear All, I am pleased to announce the release of the program RESP ESP charge Derive version III.3 (or R.E.D. III.3) and its related tools (Ante_R.E.D.-1.3 and X R.E.D. III.3) available @ http://q4md-forcefieldtools.org/RED/. New features available: - Bug corrections in R.E.D. III.2, - Portability on Windows platforms through the Cygwin environment making the R.E.D. tools fully functional on UNIX, MacIntosh and Windows operating systems (thanks to the contribution of T. Patko - California State University, Long Beach, CA, USA), - Interface of Gaussian 2009 is implemented (as for g03, g98 g94), - Improvement of GAMESS-US PC-GAMESS interface new interface for WinGAMESS, - Implementation of a new Re_Fit mode allowing charge re-fitting and force field library re-building from a previous R.E.D. run, - Development of the Mini-Howto and creation of a History file summarizing the features implemented in the R.E.D. tools, - Creation of a benchmark of charge values for models with an automatic checking procedure connection with R.E.DD.B. - New manuals (History, Howto and Guides) are available in the PDF file format. See the Documentation section from the R.E.D. web site A person who is already registered as a R.E.D.-III tools user does not need to register again: She/he can use her/his R.E.D.-III tools login/passwd obtained previously to download the R.E.D.-III.3 tools. RESP and ESP charge derivation for a new structure is an important step in molecular dynamics simulations based on AMBER, CHARMM, GLYCAM and OPLS force fields. To derive such atom-centered charges three steps need to be followed: - First, the molecule studied is optimized to determine a stable minimum (using a quantum chemistry software). - Then, this minimized structure is used to calculate a Molecular Electrostatic Potential (MEP) on a three-dimensional grid (using again a quantum chemistry software). - Finally, this grid is exported into the RESP program (also downloadable from the CCL software database) which is used to fit atom-centered charges to the MEP. Although this method is now used 'routinely' to obtain partial charges for molecules, in our opinion, it suffers from a number of limitations: - To apply this strategy, which requires the described above steps but also numerous format conversions between the different programs used, a significant number of scripts, programs and compilers are needed and used sequentially. Consequently, the procedure is tedious, time-consuming, and numerous errors can be introduced without having a real way to check them. - Although it is admitted that any quantum chemistry programs could be used to minimize the starting structure and to calculate the MEP, the Amber developers mainly use the Gaussian program, which is a quite expensive proprietary software. The GAMESS academic program, which is provided at no cost and which provide similar functionality for 'RESP' and 'ESP' charges development than Gaussian, is not officially used to derive 'RESP' or 'ESP' charges. Indeed, it is known that partial charges calculated using GAMESS, are 'different' than those determined using Gaussian. - Finally, starting from different sets of Cartesian coordinates for a same molecule, the 'RESP' or 'ESP' partial charges are, in somes cases, not reproducible even using Gaussian, making errors in the protocol difficult to detect. Thus, we developed the R.E.D. I (RESP ESP charge Derive, version 1.0) program to automatically derive 'RESP' and 'ESP' charges starting from an un-optimized PDB structure. R.E.D. sequentially executes (i) either the GAMESS program or the Gaussian program to minimize the target structure and to compute the corresponding MEP, and (ii) the RESP program to fit the atom-centered charges to the grid previously determined. Format conversions needed during the procedure and GAMESS, Gaussian and RESP inputs are automatically generated by R.E.D. By controlling the molecular orientation of the optimized geometry, a new RESP fitting procedure based on multi-orientation feature is proposed and results in highly reproducible 'RESP' and 'ESP' charges independently of the QM software or the initial Cartesian coordinate set. With R.E.D. II (version 2.0), multi-conformation RESP and ESP fit has been implemented. Such an approach permits to make the atom charge values more 'general' and effective, and is useful in molecular dynamics simulations where the whole conformational space needs to be explored. Thus with R.E.D.-II, 'multi-conformation' and 'multi-orientation' RESP fit can be performed together or independently according to the user choice. 'Standard' but also 'non-standard' RESP inputs can also be generated. Finally, RESP and ESP charges can be derived for chemical elements having up to a total number of electrons, Z = 35. With R.E.D. III.x (version 3.x), the control of charge
[gmx-users] Making Commands Non-Interactive
Dear GMX Users, I ask this question in this mailing list since probably a user have already encountered this similar problem. I would like to post-process my trajectory with the command trjconv (in mpi mode). For this I use the following shell command: echo 0 | /usr/pbs/bin/mpiexec /scratch/name/gromacs-4.0.5/bin/trjconv_mpi -s Peptide_43A1_topol.tpr -f ./XTC/Whole_Traj_43A1.xtc -o ./XTC/Whole_Traj_43A1noPBC.xtc -pbc mol -ur compact. With the selection 0 (System) It works but since my simulations is very long ( 300ns) the command stops in the middle of the trajectory before to finish the process ( i suspect a time limit for using the interactive mode). So i would like to use a script to do the task. How to pass the choice 0 in the script (i.e. equivalent to the echo 0). I use a bash shell and the command qsub to launch a mpi job. I have tried to adapt the examples available in the GMX website with a text file as suggested by the author in GROMACS site with no success. Thank you again for your help 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/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] Making Commands Non-Interactive
ABEL Stephane 175950 wrote: Dear GMX Users, I ask this question in this mailing list since probably a user have already encountered this similar problem. I would like to post-process my trajectory with the command trjconv (in mpi mode). For this I use the following shell command: Is trjconv parallelizable? This is nowhere in the documentation, but if it is, that would be very interesting... echo 0 | /usr/pbs/bin/mpiexec /scratch/name/gromacs-4.0.5/bin/trjconv_mpi -s Peptide_43A1_topol.tpr -f ./XTC/Whole_Traj_43A1.xtc -o ./XTC/Whole_Traj_43A1noPBC.xtc -pbc mol -ur compact. With the selection 0 (System) It works but since my simulations is very long ( 300ns) the command stops in the middle of the trajectory before to finish the process ( i suspect a time limit for using the interactive mode). So i would like to use a script to do the task. How to pass the choice 0 in the script (i.e. equivalent to the echo 0). I use a bash shell and the command qsub to launch a mpi job. I have tried to adapt the examples available in the GMX website with a text file as suggested by the author in GROMACS site with no success. I routinely use a text file for scripted jobs. Odd that yours isn't working. Is it just that the command still exits before finishing? In any case, you can make an .ndx file with only an entry for [System]. When presented with one choice, trjconv has to choose it. -Justin Thank you again for your help ___ 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/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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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] Making Commands Non-Interactive
Hi, Is trjconv parallelizable? This is nowhere in the documentation, but if it is, that would be very interesting... Well, the most interesting part in that regard is probably the I/O. But that's the hardest bit to parallelize. How to pass the choice 0 in the script Just as you would on the command line...: #!/bin/bash echo 0 | /usr/pbs/bin/mpiexec /scratch/name/gromacs-4.0.5/bin/trjconv_mpi -s Peptide_43A1_topol.tpr -f ./XTC/Whole_Traj_43A1.xtc -o ./XTC/Whole_Traj_43A1noPBC.xtc -pbc mol -ur compact Didn't you try? There may be a problem, as the script is probably executed in the home directory. So you need to add a line changing to the right directory; just as you have done in interactive mode. Hope it helps, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] Making Commands Non-Interactive
Justin A. Lemkul wrote: ABEL Stephane 175950 wrote: Dear GMX Users, I ask this question in this mailing list since probably a user have already encountered this similar problem. I would like to post-process my trajectory with the command trjconv (in mpi mode). For this I use the following shell command: Is trjconv parallelizable? This is nowhere in the documentation, but if it is, that would be very interesting... No. There are no 4.0.x tools that use MPI. Hence the wiki advice not to bother compiling tools in parallel, and the old website installation guide directing the use of only make mdrun after reconfiguring with --enable-mpi. echo 0 | /usr/pbs/bin/mpiexec /scratch/name/gromacs-4.0.5/bin/trjconv_mpi -s Peptide_43A1_topol.tpr -f ./XTC/Whole_Traj_43A1.xtc -o ./XTC/Whole_Traj_43A1noPBC.xtc -pbc mol -ur compact. With the selection 0 (System) It works but since my simulations is very long ( 300ns) the command stops in the middle of the trajectory before to finish the process ( i suspect a time limit for using the interactive mode). So i would like to use a script to do the task. How to pass the choice 0 in the script (i.e. equivalent to the echo 0). I use a bash shell and the command qsub to launch a mpi job. I have tried to adapt the examples available in the GMX website with a text file as suggested by the author in GROMACS site with no success. I routinely use a text file for scripted jobs. Odd that yours isn't working. Is it just that the command still exits before finishing? In any case, you can make an .ndx file with only an entry for [System]. When presented with one choice, trjconv has to choose it. Recompiling without mpi, and doing non-mdrun operations on your local machine / cluster login node is usually the approach simplest to use. Yes, it's more work when you configure and compile, but you only do that every once in a while right? 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] How x2top makes proper and improper dihedrals?
Dear all, I use x2top to get topology of a capped carbon nanotube with 168 atoms using oplsaa force field. The output information about dihedreals shows as follows. Before cleaning: 1008 dihedrals There are 252 Ryckaert-Bellemans dihedrals, 0 impropers Using my own code, I also get 1008 proper dihedrals. After comparison, I find a rule how only 252 dihedrals are keep after cleaning. For example, if I have local structure: C1 C5 \ / C3 - C4 / \ C2 C6 My own code gives 4 proper dihedrals: C1-C3-C4-C5, C1-C3-C4-C6, C2-C3-C4-C5, and C2-C3-C4-C6. And I think x2top also does in this way before cleaning. So I have question: why x2top needs a cleaning step to remove three of these four dihedrals? During cleaning, which one of four dihedrals should be kept? Also according to my understanding, for the following structure C1 - C6 / \ C2 C5 \ / C3 - C4 there should be some improper dihedrals, e.g., C1-C2-C3-C4 etc., to keep these atoms on the same plane. Why x2top does not give any improper dihedrals? Thanks in advance, Best wishes, Zhongqiao Dept of Chem Biomole National Univ of Singapore ___ 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
