Re: [gmx-users] Harmonic distance restraint during simulation
What if I want to restrain distance between two different molecules. I tried this and getting error. I looked at some previous posts and didn't find any solution to this. Some of them say it is limitation of Gromacs. Is there any way I can put distance restraint between atoms of two different molecules? Thanks in advance! Manoj Manoj Kumar Singh wrote: Hi, I want to put distance based restrain between few pairs of atoms during initial dynamics (along with Lincs on hbonds). I don't know how can I do this. Section 4.3.4 of the manual is probably a good start. -Justin I will highly appreciate any suggestion. Manoj ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Manoj Kumar Singh Graduate Student/Teaching Assistant Department of Chemistry, Clemson University Hunter Laboratories Clemson, SC 29634 [EMAIL PROTECTED] ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Coarse Grained force field
Dear users, I found MARTINI CG force fields. http://md.chem.rug.nl/~marrink/MARTINI/Parameters.html On Thu, Sep 4, 2008 at 3:14 PM, Xavier Periole [EMAIL PROTECTED] wrote: On Thu, 4 Sep 2008 14:59:55 -0400 Myunggi Yi [EMAIL PROTECTED] wrote: Dear gmx users, I'd like to run simulations with coarse grained model lipid bilayer. Where can I find the force field for coarse grain POPC lipid or equilibrated bilayer coordinates? You should first choose a coarse grained model for lipids that you found appropriate in literature and then the authors would probably give a link to the force field in the paper. If not you can always contact them. -- Best wishes, Myunggi Yi == KLB 419 Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306 Office: (850) 645-1334 http://www.scs.fsu.edu/~myunggi http://www.scs.fsu.edu/%7Emyunggi [EMAIL PROTECTED] - XAvier Periole - PhD Molecular Dynamics Group / NMR and Computation University of Groningen The Netherlands - ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Best wishes, Myunggi Yi == KLB 419 Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306 Office: (850) 645-1334 http://www.scs.fsu.edu/~myunggi [EMAIL PROTECTED] ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re[6]: Using Morse potentials with ENCAD force field
AS The system works now, thanks for finding a simple mistake. Another question I had is if I want to calculate the average velocities of all the atoms over a period of time can I use g_traj to create an average velocity of the atoms, but looking at all_veloc.xvg file the atom number starts at 0 so I don't know where to cross reference it with another file to coordinates of that atom. Is there a function in GROMACS that will give averages of velocities and positions of atoms? AS I think you can find the average atom velocity from of temperature of the system. Telling the truth I don't know why you want ones. If you tell the final result you need probably I can be of more use. I don't really remember from what number the atoms numbering starts in the programme you speak about but if it starts from zero this corresponds to the first atom in your conf.gro. AS Thanks, AS Andy -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email:[EMAIL PROTECTED] skype: vvchaban ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_energy
Hi, how does it count the drift in g_energy? What is the equation? What is the difference among fluct. and RMSD? Thanks, see you soon. ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] printing coords ; energies
Thank you. Sorry for not being clearer. I meant where in the source code are the energy related functions variables? Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Thu, Sep 4, 2008 at 16:19, Jochen Hub [EMAIL PROTECTED] wrote: Omer Markovitch wrote: Dear All, I would like to consult you on the following two things: 1) I have a small, preanalysis, routine I would like to run each time a frame is written and added to the trajectory file. After some checking, I believe that, in the file *stat.c*, the routine *void write_xtc_traj(FILE *log,t_commrec *cr, char *xtc_traj,t_nsborder *nsb,t_mdatoms *md, int step,real t,rvec *xx,matrix box,real prec)* is the routine actually printing each frame. Is this true or perhaps I've missed something? 2) Regarding energies - where are the energies stored? I mean the energy per type? The energies of the energy groups (as defined in the mdp file) are stored in the edr file (ener.edr by default). jochen In which file variable is this defined? I understand that these values are printed to the log file (usually named md.log), but I failed to locate the exact functions dealing with this. Thanks, Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Harmonic distance restraint during simulation
Manoj Kumar Singh wrote: What if I want to restrain distance between two different molecules. I tried this and getting error. I looked at some previous posts and didn't find any solution to this. Some of them say it is limitation of Gromacs. Since distance restraints are added to the topology of one molecule, I believe than can only be applied intramolecularly. -Justin Is there any way I can put distance restraint between atoms of two different molecules? Thanks in advance! Manoj Manoj Kumar Singh wrote: Hi, I want to put distance based restrain between few pairs of atoms during initial dynamics (along with Lincs on hbonds). I don't know how can I do this. Section 4.3.4 of the manual is probably a good start. -Justin I will highly appreciate any suggestion. Manoj ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Harmonic distance restraint during simulation
On Sat, 06 Sep 2008 06:13:35 -0400 Justin A. Lemkul [EMAIL PROTECTED] wrote: Manoj Kumar Singh wrote: What if I want to restrain distance between two different molecules. I tried this and getting error. I looked at some previous posts and didn't find any solution to this. Some of them say it is limitation of Gromacs. Since distance restraints are added to the topology of one molecule, I believe than can only be applied intramolecularly. Justin is right, it has to be intramolecular, but you can merge the two topologies in one and then add your distance restraint. try: pdb2gmx -merge -Justin Is there any way I can put distance restraint between atoms of two different molecules? Thanks in advance! Manoj Manoj Kumar Singh wrote: Hi, I want to put distance based restrain between few pairs of atoms during initial dynamics (along with Lincs on hbonds). I don't know how can I do this. Section 4.3.4 of the manual is probably a good start. -Justin I will highly appreciate any suggestion. Manoj ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - XAvier Periole - PhD Molecular Dynamics Group / NMR and Computation University of Groningen The Netherlands - ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Coarse Grained force field
On Sat, 6 Sep 2008 04:59:54 -0400 Myunggi Yi [EMAIL PROTECTED] wrote: Dear users, I found MARTINI CG force fields. That is the best choice you could make! :)) http://md.chem.rug.nl/~marrink/MARTINI/Parameters.html Then dig a bit in the website and you'll find everything to start a simulation. topologies, mdp, coordinates ... Heve fun, XAvier On Thu, Sep 4, 2008 at 3:14 PM, Xavier Periole [EMAIL PROTECTED] wrote: On Thu, 4 Sep 2008 14:59:55 -0400 Myunggi Yi [EMAIL PROTECTED] wrote: Dear gmx users, I'd like to run simulations with coarse grained model lipid bilayer. Where can I find the force field for coarse grain POPC lipid or equilibrated bilayer coordinates? You should first choose a coarse grained model for lipids that you found appropriate in literature and then the authors would probably give a link to the force field in the paper. If not you can always contact them. -- Best wishes, Myunggi Yi == KLB 419 Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306 Office: (850) 645-1334 http://www.scs.fsu.edu/~myunggi http://www.scs.fsu.edu/%7Emyunggi [EMAIL PROTECTED] - XAvier Periole - PhD Molecular Dynamics Group / NMR and Computation University of Groningen The Netherlands - ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Best wishes, Myunggi Yi == KLB 419 Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306 Office: (850) 645-1334 http://www.scs.fsu.edu/~myunggi [EMAIL PROTECTED] - XAvier Periole - PhD Molecular Dynamics Group / NMR and Computation University of Groningen The Netherlands - ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_energy
Hi, RMSD is your just deviation of backbone from native stare while RMS fluctuation shows the per atom deviation throughout simulation. regards, Ravi Datta Sharma Lecturer, Bioinformatics, Department of Microbiology, CCS Unversity, Meerut --- On Sat, 6/9/08, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: From: [EMAIL PROTECTED] [EMAIL PROTECTED] Subject: [gmx-users] g_energy To: gmx-users@gromacs.org Date: Saturday, 6 September, 2008, 2:41 PM Hi, how does it count the drift in g_energy? What is the equation? What is the difference among fluct. and RMSD? Thanks, see you soon. ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Unlimited freedom, unlimited storage. Get it now, on http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] trr file format
Hello, Where can I read about the exact format of the TRR and XTC files. I mean the width and type of every field in the binary trajectory file. I see read_'next_frame(status,fr)' function in 'template.c'. But where is this fuction defined? Sorry, I'm not an expert in C. :( Thanks. -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] trr file format
Vitaly Chaban wrote: Hello, Where can I read about the exact format of the TRR and XTC files. I mean the width and type of every field in the binary trajectory file. I see read_'next_frame(status,fr)' function in 'template.c'. But where is this fuction defined? Sorry, I'm not an expert in C. :( Thanks. Make your life easier by just using the supplied functions to read the files. Check any analysis program. -- 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. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
