[gmx-users] Average pdb coordinates
Dear Friends To get coordinates at specific ps i used to use following command trjconv -f md.xtc -s md.tpr -o 2000.pdb -dump 2000 *I want average pdb coordinates between 0ps to 2000ps, How i can get it ?* Regards Rituraj -- 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] Query regarding g_rmsf and g_hbond
Dear friends, I have some query regarding g_rmsf and g_hbond 1) Through g_rmsf we can plot rmsf Vs atom number (it is by default) but i want to plot rmsf Vs time, how i can do that? 2) Through g_hbond we can plot number of H-bonds Vs Time (By default) but i want to plot number of h-bonds Vs residues. Is it possible? I tried all the flag given in manual :( but i din not got desire plots. Regards Rituraj -- 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] Phosphorylation of protein
Dear friends, I want to add a phosphate (PO4) group to a amino acid residue (serine) in my protein molecule (phosphorylation of protein). Is is possible to do by in-silico (with help of Gromcs or by any other server)? Please help me in this. Thank you :) Rohan On Wed, May 19, 2010 at 7:32 PM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-us...@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: enegry minimisation (Justin A. Lemkul) 2. g_cluster, RMSD distribution (Micha? Koli?ski) 3. Re: enegry minimisation (Gaurav Goel) 4. Re: Re: crystallographic water to tip4p model (? ?) 5. Re: enegry minimisation (sonali dhindwal) -- Message: 1 Date: Wed, 19 May 2010 09:18:08 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] enegry minimisation To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4bf3e510.3040...@vt.edu Content-Type: text/plain; charset=windows-1252; format=flowed Gaurav Goel wrote: After adding water you can do energy minimization (EM) in two steps: 1. Constrain the protein backbone and do EM. 2. Now do EM on the full system. 3. Run a short MD simulation by constraining the protein backbone. The above three steps will help hydrate the protein molecule with minimal distortion of protein structure. Such finesse may certainly be beneficial. Just for clarity, though, what you are referring to is the application of (position) restraints, not constraints. http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints -Justin 4. Now run a MD on full system. for details looks here: http://www.google.com/url?sa=tsource=webct=rescd=2ved=0CBcQFjABurl=http%3A%2F%2Feugen.leitl.org%2Fchem%2Fkerrigje%2Fpdf_files%2Ffwspidr_tutor.pdfei=jOPzS8a3Lab2MdX1_aAOusg=AFQjCNGB_3mXSQRHuqehBSHXsRyXP1Gymgsig2=bY3NqXHmruR7eSLVyAuCHQ http://www.google.com/url?sa=tsource=webct=rescd=2ved=0CBcQFjABurl=http%3A%2F%2Feugen.leitl.org%2Fchem%2Fkerrigje%2Fpdf_files%2Ffwspidr_tutor.pdfei=jOPzS8a3Lab2MdX1_aAOusg=AFQjCNGB_3mXSQRHuqehBSHXsRyXP1Gymgsig2=bY3NqXHmruR7eSLVyAuCHQ -Gaurav On Wed, May 19, 2010 at 8:18 AM, sonali dhindwal sonali11dhind...@yahoo.co.in mailto:sonali11dhind...@yahoo.co.in wrote: Sorry, but I couldnt get your question, I have used this .mdp file for energy minimisation after addition of water and using GROMOS96 43a1 force field : title = drg_trp cpp = /lib/cpp ; location of cpp on SGI define = -DFLEX_SPC ; Use Ferguson’s Flexible water model [4] constraints = none integrator = steep dt = 0.002 ; ps ! nsteps = 2000 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME ; Use particle-mesh ewald rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 I hope it will help you to guide me further Thanks -- Sonali Dhindwal --- On *Wed, 19/5/10, Erik Marklund /er...@xray.bmc.uu.se mailto:er...@xray.bmc.uu.se/* wrote: From: Erik Marklund er...@xray.bmc.uu.se mailto:er...@xray.bmc.uu.se Subject: Re: [gmx-users] enegry minimisation To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Date: Wednesday, 19 May, 2010, 5:31 PM sonali dhindwal skrev: Hello All This question may sound trivial to many, but as i am new to this field, please help. I want to ask a question regarding my previous query of distortion of protein strucutre after molecular dynamcs simulation. I have noticed that after enegry minimisation using steepest decent algorithm, using emtol of 1000 kJ mol^-1 nm^-1 , large amount of distortion occurs. So is it necessary to do enegry minimisation step before MD, because this is my modeled protein, and i have already done energy minimisation using different program and after that I
[gmx-users] PCA tutorial
Dear friends, I want to do PCA for my MD data. If anybody know the tutorial regarding PCA, please let me know. Thanks in advanced Regard Rohan On 2/1/10, gmx-users-requ...@gromacs.org gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: error: Cannot compile and link MPI code with mpicc (Mark Abraham) 2. Re: Re : MPI (Mark Abraham) 3. H2 topology (011013021-Jyotsna) 4. Re: H2 topology (David van der Spoel) 5. tutorial for ionic liquid (Catarina Nunes) 6. Re: tutorial for ionic liquid (Justin A. Lemkul) 7. non-equilibrium MD simulations (oguz gurbulak) 8. Re: non-equilibrium MD simulations (Justin A. Lemkul) -- Message: 1 Date: Mon, 01 Feb 2010 22:32:35 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] error: Cannot compile and link MPI code with mpicc To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4b66bbd3.3030...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 01/02/10 20:19, Sarath Kumar wrote: Message: 2 Date: Mon, 1 Feb 2010 12:31:32 +0530 From: Chandan Choudhury iitd...@gmail.com mailto:iitd...@gmail.com Subject: Re: [gmx-users] error: Cannot compile and link MPI code with mpicc To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4e22679c1001312301x5ee854dbn401b1e11f8d4b...@mail.gmail.com mailto:4e22679c1001312301x5ee854dbn401b1e11f8d4b...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Thanks. I just added export CPPFLAGS=-I/usr/local/openmpi/include in the bashrc file, and could compile the mpi version of gromacs. The next thing is I got the error on executing mdrun_mpi -h Following is the output. Kindly help. corsica:/usr/local/gromacs/bin # mdrun_mpi -h [corsica:17130] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182 -- It looks like orte_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during orte_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): orte_rml_base_select failed -- Returned value -13 instead of ORTE_SUCCESS -- -- It looks like MPI_INIT failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during MPI_INIT; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): ompi_mpi_init: orte_init_stage1 failed -- Returned Not found (-13) instead of Success (0) -- *** An error occurred in MPI_Init *** before MPI was initialized *** MPI_ERRORS_ARE_FATAL (goodbye) [corsica:17130] Abort before MPI_INIT completed successfully; not able to guarantee that all other processes were killed! -- Chandan kumar Choudhury NCL, Pune INDIA U will be getting error s like this as the MPI failed. When u run mdrun with MPI. If u use this CPPFLAGS, and i also had a problem. When i used this option, after that i was unable to revert back it to the original state also. So the better option update the gcc, c++ compilers, If u have doubt in this, remove gromacs, All MPi. then do yum install -y *openmpi* --It will automatically install the missing libraries in dependencies. and then download fftw ---latest the install fftw with ./configure --enable-threads --enable-mpi the gromacs ./configure --enable-threads --enable-mpi this will surely work, because in order gromacs work with MPI. U should compile fftw with MPI as
[gmx-users] Plot renumbering
Hello friends, As Justin replied at carla query about structure deformation after the pdb2gmx the new number retain till end. My PDB starts at 24 to 200 aa, While running xmgrace (after complete simulation) the rmsd plot is from 1 to 176aa. I understood by previous mail that gromacs renumbered my pdb file at first step. My question is, Is their any way to get plot from 24 to 200 (as entry in pdb) rather 1 to 174 ? Regard Rituraj On Fri, Jan 29, 2010 at 7:28 PM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: Structure deformation (Carla Jamous) 2. Re: Structure deformation (Justin A. Lemkul) 3. Re: Re: including a custom itp file in topology (Tsjerk Wassenaar) 4. Re: RE: xmgrace (bharat gupta) 5. Re: RE: xmgrace (Justin A. Lemkul) 6. Re: RE: xmgrace (Baofu Qiao) -- Message: 1 Date: Fri, 29 Jan 2010 14:03:12 +0100 From: Carla Jamous carlajam...@gmail.com Subject: Re: [gmx-users] Structure deformation To: jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: e02c90f11001290503yce52eb7w45f7f23a53250...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Thank you Justin, you were right I was looking at the wrong residue numbers. I have another question that may also sound stupid, but I can't figure it out: I want to extract from my trajectory, the protein, the ligand and ions. However, when I try to do that with trjconv -f .trr -s .trr -n .ndx gromacs asks to choose a group from my index file. But if I choose group 0 1 2 it only takes the first group without the rest. So how can I extract many groups at once from my trajectory? Carla On Fri, Jan 29, 2010 at 12:48 PM, Justin A. Lemkul jalem...@vt.edu wrote: Carla Jamous wrote: Hi everyone, I have a question about structure deformation Can pdb2gmx alter secondary structures of my protein, while adding hydrogens. Because I had a helix in my protein, that became a beta-sheet after pdb2gmx. Sorry to say, but this sounds completely unlikely. A bug of this magnitude surely would've been noticed long ago. What may be the problem? Are you certain you're looking at the same residues? pdb2gmx renumbers from 1, so if there are missing N-terminal residues, they will not have the same numbers before and after pdb2gmx. -Justin Thank you Carla -- 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 -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100129/55ff7a64/attachment-0001.html -- Message: 2 Date: Fri, 29 Jan 2010 08:04:11 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Structure deformation To: Gromacs Users' List gmx-users@gromacs.org Message-ID: 4b62dccb.8030...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Carla Jamous wrote: Thank you Justin, you were right I was looking at the wrong residue numbers. I have another question that may also sound stupid, but I can't figure it out: I want to extract from my trajectory, the protein, the ligand and ions. However, when I try to do that with trjconv -f .trr -s .trr -n .ndx gromacs asks to choose a group from my index file. But if I choose group 0 1 2 it only takes the first group without the rest. So how can I extract many groups at once from my trajectory? Use make_ndx to merge the desired groups (i.e., 0 | 1 | 2) or simply !12 (assuming group 12 is SOL). -Justin Carla On Fri, Jan 29, 2010 at 12:48 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Carla Jamous wrote: Hi everyone,
[gmx-users] Problem in g_rms
I want get rmsd deviation between NMR structure and the simulated result, but i am getting following error in following command. g_rms -s em.tpr -f md.trr -o rsmd_Calpha.xvg WARNING: topology has 50772 atoms, whereas trajectory has 22899 --- Program g_rms, VERSION 4.0.5 Source code file: mshift.c, line: 103 Fatal error: Molecule in topology has atom numbers below and above natoms (22899). You are probably trying to use a trajectory which does not match the first 22899 atoms of the run input file. You can make a matching run input file with tpbconv. --- I want to analyze RMSD of backbone atoms. They mention about tpbconv, How i can use it to sort it out ? Please help me.. Regards Rituraj -- 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] position restrained dynamics protein size
this: ... 66ASN O 671 3.212 3.554 5.248 66ASN HO 672 3.258 3.625 5.302 1DPP C33 673 0.623 5.221 1.344 1DPP C34 674 0.461 5.360 1.434 1DPP C35 675 0.697 5.438 1.420 1DPP N 676 0.604 5.327 1.444 1DPP C32 677 0.607 5.278 1.583 1DPP C31 678 0.722 5.193 1.637 1DPP O32 679 0.860 5.229 1.645 1DPP P 680 0.954 5.102 1.677 1DPP O33 681 0.882 4.986 1.620 1DPP O34 682 1.094 5.137 1.647 1DPP O31 683 0.929 5.088 1.836 1DPP C3 684 1.003 5.184 1.912 1DPP C2 685 0.946 5.209 2.052 1DPP O21 686 0.988 5.332 2.111 1DPP C21 687 0.939 5.454 2.087 1DPP O22 688 0.893 5.479 1.976 1DPP C22 689 0.952 5.554 2.195 1DPP C23 690 1.086 5.626 2.185 1DPP C24 691 1.132 -0.046 2.310 1DPP C25 692 1.029 0.049 2.372 1DPP C26 693 1.080 0.108 2.504 1DPP C27 694 1.100 0.015 2.624 1DPP C28 695 1.147 0.089 2.750 1DPP C29 696 1.047 0.189 2.809 1DPPC210 697 1.127 0.248 2.925 1DPPC211 698 1.046 0.363 2.985 1DPPC212 699 1.127 0.411 3.105 1DPPC213 700 1.093 0.323 3.226 1DPPC214 701 1.141 0.402 3.348 1DPPC215 702 1.107 0.339 3.483 1DPPC216 703 1.135 0.428 3.604 1DPP C1 704 0.997 5.089 2.132 1DPP O11 705 0.921 5.069 2.251 1DPP C11 706 0.969 4.974 2.332 1DPP O12 707 1.070 4.914 2.295 1DPP C12 708 0.886 4.938 2.449 1DPP C13 709 0.889 4.790 2.488 1DPP C14 710 0.996 4.756 2.592 1DPP C15 711 0.985 4.603 2.597 1DPP C16 712 1.098 4.556 2.689 1DPP C17 713 1.061 4.414 2.730 1DPP C18 714 1.174 4.351 2.813 1DPP C19 715 1.189 4.364 2.965 1DPPC110 716 1.330 4.335 3.017 1DPPC111 717 1.367 4.338 3.165 1DPPC112 718 1.514 4.304 3.191 1DPPC113 719 1.542 4.329 3.339 1DPPC114 720 1.691 4.329 3.372 1DPPC115 721 1.711 4.346 3.523 1DPPC116 722 1.861 4.344 3.549 1DPP C33 723 1.394 3.827 1.098 1DPP C34 724 1.402 3.868 1.324 1DPP C35 725 1.337 3.651 1.249 1DPP N 726 1.324 3.795 1.223 1DPP C32 727 1.185 3.841 1.213 1DPP C31 728 1.074 3.797 1.309 1DPP O32 729 1.100 3.828 1.446 1DPP P 730 1.029 3.739 1.561 1DPP O33 731 0.892 3.693 1.529 1DPP O34 732 1.132 3.642 1.606 1DPP O31 733 1.020 3.846 1.680 1DPP C3 734 1.118 3.824 1.782 1DPP C2 735 1.123 3.924 1.898 1DPP O21 736 1.254 3.939 1.955 1DPP C21 737 1.326 4.049 1.942 You see that starting from the second nitrogen atom of my DPPC molecules, the residue number should be 68 and not 2. So this is what trjconv is actually giving me. It is renumbering the solvent molecules but it is not recognising different DPPC molecules. Instead it is writing my DPPC membrane as one single huge molecule. _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100119/5d819194/attachment.html -- -- 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! End of gmx-users Digest, Vol 69, Issue 88 * -- -- RITURAJ PUROHIT Assistant Professor, Bioinformatics Division School of Bio-sciences and Technology (SBST) Vellore Institute of Technology, University Address: SBST, VIT University, Vellore-632014,Tamilnadu, India. Phone: +91-416-2202638 (Lab), +91-9944649073 (Mobile) Fax; +91-416-2243092, E-mail: ritu...@vit.ac.in -- The future belongs to those who believe in the beauty of their dreams. -- 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
[gmx-users] Re: Regarding g_rmsf
-users@gromacs.org Message-ID: f2be40f50912150052l6f04594ct5817933f4bae8...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Dear all, my self ashish and i am trying to dynamics using gromacs. i am new in these field. in the time of running Pdb2gmx to create .gro file. i am geting these error. Fatal error: Atom HA in residue MET 1 not found in rtp entry with 9 atoms please help me sortout these problem. -- Ashish Pandey NIPER India -- Message: 6 Date: Tue, 15 Dec 2009 10:03:29 +0100 From: XAvier Periole x.peri...@rug.nl Subject: Re: [gmx-users] Hi To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: f925b208-9bf1-4c79-ac31-58e22b739...@rug.nl Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes try the option -ignh, it will ignore the the hydrogen atoms in your pdb file and generate the ones necessary to the force field you choose. On Dec 15, 2009, at 9:52 AM, ashish pandey wrote: Dear all, my self ashish and i am trying to dynamics using gromacs. i am new in these field. in the time of running Pdb2gmx to create .gro file. i am geting these error. Fatal error: Atom HA in residue MET 1 not found in rtp entry with 9 atoms please help me sortout these problem. -- Ashish Pandey NIPER India -- 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 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! End of gmx-users Digest, Vol 68, Issue 77 * -- -- RITURAJ PUROHIT Assistant Professor, Bioinformatics Division School of Bio-sciences and Technology (SBST) Vellore Institute of Technology, University Address: SBST, VIT University, Vellore-632014,Tamilnadu, India. Phone: +91-416-2202638 (Lab), +91-9944649073 (Mobile) Fax; +91-416-2243092, E-mail: ritu...@vit.ac.in -- The future belongs to those who believe in the beauty of their dreams. -- 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] Re: xmgrace plot
: Jon Fuller jonathan.ful...@gmail.com Subject: Re: [gmx-users] xmgrace plot To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 76dd1c620912080253t6b8ce2dehfa65e42bda43a...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 From the command line you can type xmgrace file1.xvg file2.xvg (where file1 and file2 are the filenames!). Jon 2009/12/8 Henry Yang henryy...@yahoo.com Hello everyone, I am also new to xmgrace. I have two .xvg file which I have got from the simulation data analysis. How can I open both of them in one xmgrace graph with two distinct color? How can I proceed with the comand? I know this is very basic but I have to learn! Pls give me response. Henry Biochemistry -- 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 -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20091208/a1d92248/attachment-0001.html -- -- 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! End of gmx-users Digest, Vol 68, Issue 44 * -- -- RITURAJ PUROHIT Assistant Professor, Bioinformatics Division School of Bio-sciences and Technology (SBST) Vellore Institute of Technology, University Address: SBST, VIT University, Vellore-632014,Tamilnadu, India. Phone: +91-416-2202638 (Lab), +91-9944649073 (Mobile) Fax; +91-416-2243092, E-mail: ritu...@vit.ac.in -- The future belongs to those who believe in the beauty of their dreams. -- 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] RMSD Vs Residue no by Grace
Dear friends, I am able to plot, RMSD between Time (ps) by following command by using GRACE.. g_rms -s md.tpr -f md.xtc xmgrace rmsd.xvg How we can I plot a graph betwwen RMSD and residue no ..?? My aim is to find RMSD at each residues. How i can do that? looking forward for u r important suggestions. Thanking you Regards Rituraj -- 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 to neutralize net charge of protein and why
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 _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20090829/a806db6e/attachment-0001.html -- ___ 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! End of gmx-users Digest, Vol 64, Issue 198 ** -- -- RITURAJ PUROHIT Assistant Professor, Bioinformatics Division School of Bio-sciences and Technology (SBST) Vellore Institute of Technology, University Address: SBST, VIT University, Vellore-632014,Tamilnadu, India. Phone: +91-416-2202638 (Lab), +91-9944649073 (Mobile) Fax; +91-416-2243092, E-mail: ritu...@vit.ac.in -- The future belongs to those who believe in the beauty of their dreams. ___ 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] DSSP problem
Dear all I want ti install DSSP for visualization of secondary structure in gromacs analysis. I am doing following procedure.. Copy the executable dsspcmbi to /usr/bin or /usr/local/bin ln -s dsspcmbi dssp And running it for my Pdb like that dssp file.pdb file.dssp BUt I am getting error Permission Denied even i m super user for the machine (root). [r...@localhost ~]# dssp bash: /usr/local/bin/dssp: Permission denied [r...@localhost ~]# Plaese any body tell the solution for this problem... Regard Rituraj -- The future belongs to those who believe in the beauty of their dreams. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] DSSP problem
Dear mark Where i can get the file with permission. I downloaded from http://swift.cmbi.kun.nl/gv/dssp/ Rituraj On 6/4/09, gmx-users-requ...@gromacs.org gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: PME on BlueGene (Mark Abraham) 2. about PMF calculation (mirc...@sjtu.edu.cn) 3. Replacing the PRODRG charges (Lucio Ricardo Montero Valenzuela) 4. Re: Replacing the PRODRG charges (Mark Abraham) 5. how to include ionic strength (amri ta) 6. Re: how to include ionic strength (Mark Abraham) 7. DSSP problem (rituraj purohit) 8. Re: DSSP problem (Mark Abraham) -- Message: 1 Date: Thu, 04 Jun 2009 11:06:16 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] PME on BlueGene To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4a271e08.2090...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed Jakob Wohlert wrote: Mark Abraham wrote: Jakob Wohlert wrote: Hi, I'm trying to compile Gromacs 4.0.4 for BlueGene/P, and using the configuration options from the wiki I have succeeded insofar that I have a working program as long as I don't use PME. I have tried many different variants of fftw - 2.1.5, 3.2.1, single precision, double precision, different compiler optimizations and so on, but it all ends the same: mdrun getting stuck somewhere in the initialization process. However, by using the built in fft library FFTPACK instead of FFTW, PME will work, but that is not really an alternative. In at least a few cases I have been able to pinpoint the location where it hangs - it's in pme.c, subroutine pme_dd_sendrecv. The program calls MPI_Sendrecv, but then nothing else happens as far as I can tell. I'm confused and I have sort of ran out of ideas right now. Has anyone else encountered a problem like this, or has anyone any suggestions how to proceed from here? Thanks for your answer! That looks to me like the separate PME nodes are dying through some linking problem and the problem is only manifest on node 0 when its sendrecv doesn't complete. Forcing mdrun -npme 0 may confirm this when all the nodes die at the first point they refer to a symbol in the FFT library. Otherwise, looking at warnings/errors from the linker will be required. Ok, can you be a little more specific? Do you mean when compiling fftw, gromacs or both? I'm not very experienced with these kind of things. GROMACS links with the FFTW library, so there ought to be warnings of potential problems at link time, i.e. the final stage of a GROMACS make mdrun (having started with a clean configuration, either freshly unpacked or after make clean). The last 100 or so lines of the output of make mdrun should have any relevant data. Are you compiling an FFT library version for the back end, or the front end? I'm trying to get it to work on the back end, on the front end it works fine! (So, I have fftw libraries for both). My BG/L FFTW-3.2 configure line is ../configure --prefix /hpc/home/mja163/progs CC=blrts_xlc --host=powerpc --build=ppc64 CFLAGS=-qbgl -qarch=440d -qtune=440 -qnoautoconfig -O5 --disable-fortran --enable-float but you may need to tweak that for BG/P for all I know. Let me know when/if something works and I'll update the wiki. Mark -- Message: 2 Date: Thu, 04 Jun 2009 13:56:51 +0800 From: mirc...@sjtu.edu.cn Subject: [gmx-users] about PMF calculation To: gmx-users@gromacs.org Message-ID: 20090604135651.2wdhcqo28csw8...@webmail1.sjtu.edu.cn Content-Type: text/plain; charset=GB2312; DelSp=Yes; format=flowed Dear All: I want to do some PMF (Potenial of Mean Force) calculation by AFM pulling method using the pull code to study the unbinding of a protein and a ligand. I want pull the ligand from its binding site and calculate the PMF of the procedure, does it possible? I have read the user manual about PMF calculation carefully, but still not clear how to do . Does anyone have any tutorial about how to do this kind of calculation or any published papers doing this things? anyhelp is greatly appreciate! Best Wishes R-X Gu -- Message
[gmx-users] Gromacs output analysis
Hello to everybody I need the gromacs analysis document. I mean i want to do analysis (like; RMSD, traj)of my result which I got after simulation of protein molecule. If anybody having any PDF or web link emphasis the analysis part, please forword me... Thank you Rituraj On Wed, Jun 3, 2009 at 9:05 PM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. protein running out of box (sheerychen) 2. Re: protein running out of box (Justin A. Lemkul) 3. Re: protein running out of box (ravi sharma) 4. spc.itp for the amber force field (Rebeca Garc?a Fandi?o) 5. Some questions regarding generating topologies (Manik Mayur) 6. Re: Some questions regarding generating topologies (Justin A. Lemkul) -- Message: 1 Date: Wed, 3 Jun 2009 15:37:57 +0200 From: sheerychen sheeryc...@gmail.com Subject: [gmx-users] protein running out of box To: gmx-users@gromacs.org Message-ID: e1b92dfb0906030637y6cc57951oaf959aafd2b46...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hello, every body. I have running a MD for 10ns. However, after 5ns part of protein will running out of the box and be located at other part of the water box. And the whole structure seems ver strange. It seems that it was caused by the mass translation but I have used the comm_mode=Linear. Any suggestions? -- Zhen Chen, Department of Bioprocess and Biosystem Engineering, Hamburg University of Technology, Denickestr. 15, D-21071, Hamburg,Germany Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail: zhen.c...@tuhh.de -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090603/20c8cd2e/attachment-0001.html -- Message: 2 Date: Wed, 03 Jun 2009 09:46:08 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] protein running out of box To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4a267ea0.8090...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed sheerychen wrote: Hello, every body. I have running a MD for 10ns. However, after 5ns part of protein will running out of the box and be located at other part of the water box. And the whole structure seems ver strange. It seems that it was caused by the mass translation but I have used the comm_mode=Linear. Any suggestions? What you are seeing is a normal consequence of periodicity. There is no side in an infinite system: http://oldwiki.gromacs.org/index.php/Periodic_Boundary_Conditions -Justin -- Zhen Chen, Department of Bioprocess and Biosystem Engineering, Hamburg University of Technology, Denickestr. 15, D-21071, Hamburg,Germany Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail: zhen.c...@tuhh.de mailto:zhen.c...@tuhh.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- Message: 3 Date: Wed, 3 Jun 2009 07:07:57 -0700 (PDT) From: ravi sharma rdsharma...@yahoo.com Subject: Re: [gmx-users] protein running out of box To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 147031.55861...@web54606.mail.re2.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Dear Zhen Chen Protein is located stranger(sometime at the one side of the protein,in other frame other side). Its not a problem. Your simulation is fine. it is due to you had given PBC. thats why. You can reset your trejectory using trjconv. regards Ravi Datta Sharma Lecturer, Bioinformatics, Department of Microbiology, CCS Unversity, Meerut --- On Wed, 3/6/09, sheerychen sheeryc...@gmail.com wrote: From:
[gmx-users] Problem in fianl step of MD
Hi .. I am using gromacs 4.0 for simulating a protein molecule. i am getting following problem during md run[md.mdp dt =0.002 ; ps ! nsteps = 10 ; total 200.0 ps ] t = 47.530 ps: Water molecule starting at atom 46763 can not be settled. Check for bad contacts and/or reduce the timestep. What should i have to do ? please help me.. Rituraj ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
