[gmx-users] free energy calculation
Dear all, Can anybody tell me how to calculate the free energy difference after running simulation with lamda(0, 0.1,...1)? I am following the tutorial on wiki, but i have no idea about the details to do the data analysis. any software can do it? and any reference for the instruction? I am new here. thanks a lot Qiang ___ 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] About g_msd
Hi Justin, Wohlert and Edholm (http://dx.doi.org/10.1063/1.2393240) suggested to extract the motion of the 2 monolayers relative to each other, before calculating the MSD. This is an artefact coming from the finite size of computer simulations. This may explain the discrepancy you get between both leaflets. Second, they showed that there are two different diffusions. A fast diffusion occuring on ps time scale and a longer one which is brownian and can be compared to FRAP experiments. In their paper, they propose a fitting procedure that extracts both diffusion constants. Furthermore, be sure to equilibrate enough (a few tens of ns) before doing this analysis. Cheers, Patrick Justin A. Lemkul a écrit : Hi Alan, Thanks for the reply. My initial trajectory showed several of the lipids jumped across the box and continued through the bilayer from there, which resulted in a large displacement, so I processed the trajectory with trjconv -pbc nojump. There is still a rather large initial displacement (within the first several nanoseconds out of 100, likely due to my equilibration procedure of packing the lipids tightly around the peptide), so I attempted to analyze the last 75 ns and 90 ns of the trajectory, using the structures at those times as the reference (in g_msd -s). Still the same result, a large value of D. Any ideas? Thanks again. -Justin Quoting Alan Dodd [EMAIL PROTECTED]: What happens if you visualise the trajectory? Two orders of magnitude in scale of lipid movement should stick out like a sore thumb. - Original Message From: Justin A. Lemkul [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Wednesday, January 16, 2008 12:27:45 AM Subject: [gmx-users] About g_msd Hello again, I'm back with a few more questions about g_msd (version 3.3, in case I hadn't mentioned that before). Thanks to Xavier's message earlier, I have abandoned use of ordered trajectories to analyze my lipids. I will deal with lipid shells in the future. For now I am approaching the problem of lateral diffusion coefficients from a slightly different angle. My system contains a helical peptide that is oriented asymmetrically with respect to the DPPC bilayer. It is tilted and only partially embedded into the intracellular leaflet of the bilayer (at the beginning of the simulation). Due to the asymmetry, I would like to study the properties of the leaflets separately, including, among other parameters, the lateral diffusion coefficients of the component lipids. I have found a few papers that have simulated pure DPPC bilayers, and am using them as somewhat of a reference point for the magnitude of the lateral diffusion coefficients that I am determining: E. Lindahl and O. Edholm (2001) J. Chem. Phys. 115 (10), and U. Essmann and M. L. Berkowitz (1999) Biophys. J. 76. For the top leaflet of my bilayer, I am getting a value of D = (4.0+/-2.2)x10^-7 cm^2/sec (reasonable, in terms of order of magnitude, I think), but for the bottom leaflet, I am getting roughly (355.7+/-551.5)x10^-7 cm^2/sec. I figured this enormous number was due to artefacts of PBC, so I tried every iteration of trjconv -pbc, but to no avail. Every result is quite similar. I tried starting g_msd at a later time (10 ns, 25 ns) to determine if any large initial movements of lipids were responsible for the result, but I'm still coming up with the enormous value of D (albeit slightly lower, ~200+/-400) I am using g_msd -mol, with an index file that contains molecule numbers, and then using g_analyze on the output .xvg file to get the values of D. Has anyone ever experienced anything similar? Am I missing something obvious? Thanks in advance, as always, especially if you read the entirety of my lengthy message. -Justin Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (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 Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs ___ 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
Re: [gmx-users] interchain bond
Xavier Periole wrote: On Tue, 15 Jan 2008 16:32:54 +0100 Velia Minicozzi [EMAIL PROTECTED] wrote: Dear gromacs users, I have two identical peptides which should bind one metal ion. I guess I have not understood how I can make this bond. I labeled the two peptides with different chain identifier otherwise pdb2gmx does not understand that they are two peptides and not one protein. The metal is labeled with a third identifier, and I modified the ffoplsaabon.itp file inserting this bond and the specbond.dat file. Having 3 chains I have 3 different itp files and one top file in which all of the itp are called. Unfortunately in none of the itp files nor in the top file there is any reference to this bond I created, and after some time of MD simulation two of the atoms bound to the metal fly away even if I use constraints on all bonds. You have to use the merge option of pdb2gmx, it will generate one topology of the two peptides and the metal. Then you can add the bond within this topology file. The numbering of the atoms is important. If you create a chemical bond between two topologies (peptide-metal) this will not work. Maybe you want to create a bond of type 6. Such bonds will not be constrained with LINCS but restrain your metal ions to the peptides with a real harmonic potential... Cheers, Jochen I guess I didn't create those bonds correctly. How should I do? Any help is welcome! Best, Velia ___ 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 NMR Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ 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 . -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] charmm force field
hi, This is not specificaly A GROMACS related question. I want to do MD simulations using CHARMM force field using GROMACS. I am aware of the perl programs written by M. ABRAHAM and look forward to using it. I want to know which is the most convenient way in which I can get the CHARMM force field input file. thanks ___ 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] how to get charmm force field input file for MD
hi, This is not specificaly A GROMACS related question. I want to do MD simulations using CHARMM force field using GROMACS. I am aware of the perl programs written by M. ABRAHAM and look forward to using it. I want to know which is the most convenient way in which I can get the CHARMM force field input file. thanks___ 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: free energy calculation
Dear all, Can anybody tell me how to calculate the free energy difference after running simulation with lamda(0, 0.1,...1)? I am following the tutorial on wiki, but i have no idea about the details to do the data analysis. any software can do it? and any reference for the instruction? I am new here. thanks a lot Qiang Try to read this: http://en.wikipedia.org/wiki/Numerical_integration Vojtech Spiwok winmail.dat___ 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] polyatomic ion additon by genion
Hi all, I have been trying to simulate peptide in water box with guanidium ion thiocynate ion(SCN-).I tried to add these ion by genion command line by simply adding topology information of these ion in ions.itp of gromacs library directory but it is not working properly it only adds one atom by replacing water molecule it seems that genion is applicable only for monoatomic ion. If i have to do simulation with these polyatomic ions with perticular salt concentration how do i will perform it. Kinshuk IIT-Bombay India ___ 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] polyatomic ion additon by genion
[EMAIL PROTECTED] wrote: Hi all, I have been trying to simulate peptide in water box with guanidium ion thiocynate ion(SCN-).I tried to add these ion by genion command line by simply adding topology information of these ion in ions.itp of gromacs library directory but it is not working properly it only adds one atom by replacing water molecule it seems that genion is applicable only for monoatomic ion. If i have to do simulation with these polyatomic ions with perticular salt concentration how do i will perform it. with genbox. compute number yourself. Kinshuk IIT-Bombay India ___ 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 -- David van der Spoel, Ph.D. 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
[gmx-users] Re: how to create tpr file from pdb created with Hyperhem for using with OPLS
Thanks Mark, but your first answer didn't help me at all. I want to create pdb manually which will work with gromacs pdb2gmx comand in order to get gro and top using OPLS, and seeking for some clues. It doesn't matter if it is Hyperchem or JME or MOL, I need a proper pdb which will be understandable to Gromacs. I know that PRODGR is not compatible with OPLS, that's why I am asking how to change gro and top to enable them to be compatible with OPLS The same story and with beta files (with ff43a1.itp) I'm trying to run MD using OPLS with my own molecule solved in the water, for that I was trying to create mymolecule.itp database file, and in order to do so I need to know how to describe correctly dihedrals (in OPLS standart) 'what indicates?' it's just simple logic if I use edited on Windows files to produce new gro and updated top files on Unix, that indicates to me that cpp have no errors in reading these files (may be I am wrong, because I do not know how these files are processed during each of these precesses - like genbox and editconf, probably it's different from grompp?). number of molecules of whater in top x3+1(my molecule)xn(number of atoms in that molec.)=total nr of atoms in gro file. (it would be in gro let's say 1500 atoms, and in top let's say DGR=1 and SOL=490). I know exist some short instructions how to do so, but I couldn't find them in the manual. P.S.these links provided are pointing to the empty sites. - Looking for last minute shopping deals? Find them fast with Yahoo! Search.___ 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] how to get charmm force field input file for MD
sarbani chattopadhyay wrote: hi, This is not specificaly A GROMACS related question. I want to do MD simulations using CHARMM force field using GROMACS. I am aware of the perl programs written by M. ABRAHAM and look forward to using it. I want to know which is the most convenient way in which I can get the CHARMM force field input file. Google will find the official CHARMM force fields. Various modified versions etc. might best be obtained from the websites of the authors of the papers that describe them. Mark ___ 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] Re: how to create tpr file from pdb created with Hyperhem for using with OPLS
Egidijus Kuprusevicius wrote: Thanks Mark, but your first answer didn't help me at all. I want to create pdb manually which will work with gromacs pdb2gmx comand in order to get gro and top using OPLS, and seeking for some clues. It doesn't matter if it is Hyperchem or JME or MOL, I need a proper pdb which will be understandable to Gromacs. We being asked about converting .ent formats :-) I think I suggested as good a strategy as any. About a minute's googling reveals that Hyperchem can write a .pdb format. I know that PRODGR is not compatible with OPLS, that's why I am asking how to change gro and top to enable them to be compatible with OPLS That's a better question. Atom names and residue names need to be consistent with what is in the force field files. There are standard names for these, and if your PDB-generator uses them then you can feed them to pdb2gmx, choose oplsaa and probably do OK. PRODRG is useless here. If you need non-standard residues, then see the GROMACS wiki page on Parameterization. The same story and with beta files (with ff43a1.itp) I'm trying to run MD using OPLS with my own molecule solved in the water, for that I was trying to create mymolecule.itp database file, and in order to do so I need to know how to describe correctly dihedrals (in OPLS standart) Chapter 5 in the manual describes the format, chapter 4 describes the functions the format defines. 'what indicates?' it's just simple logic if I use edited on Windows files to produce new gro and updated top files on Unix, that indicates to me that cpp have no errors in reading these files (may be I am wrong, because I do not know how these files are processed during each of these precesses - like genbox and editconf, probably it's different from grompp?). When replying to someone, please quote their words so that people know what you're talking about. I partly remember, because I wrote them, but hardly anybody else will. number of molecules of whater in top x3+1(my molecule)xn(number of atoms in that molec.)=total nr of atoms in gro file. (it would be in gro let's say 1500 atoms, and in top let's say DGR=1 and SOL=490). I know exist some short instructions how to do so, but I couldn't find them in the manual. P.S.these links provided are pointing to the empty sites. I can't remember what you're talking about here. Mark ___ 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] About g_msd (and noise)
I've been playing with g_msd myself recently, and been seeing weird results toward the end of the simulation. From the below post, it looks like I was doing it correctly (apart from analysing the leaflets separately). Previous posts in the mailing list have implied that increased noise towards the end of a simulation is inherent in the algorithm, I just wanted to check that I was interpreting those posts correctly? And if this is so, do people just not show the results towards the end? - Original Message From: David van der Spoel [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, January 16, 2008 6:48:32 AM Subject: Re: [gmx-users] About g_msd Justin A. Lemkul wrote: Hi Alan, Thanks for the reply. My initial trajectory showed several of the lipids jumped across the box and continued through the bilayer from there, which resulted in a large displacement, so I processed the trajectory with trjconv -pbc nojump. There is still a rather large initial displacement (within the first several nanoseconds out of 100, likely due to my equilibration procedure of packing the lipids tightly around the peptide), so I attempted to analyze the last 75 ns and 90 ns of the trajectory, using the structures at those times as the reference (in g_msd -s). Still the same result, a large value of D. Any ideas? please go back to your original trajectory and do normal g_msd for the P atoms only. (no mol flags etc.) Thanks again. -Justin Quoting Alan Dodd [EMAIL PROTECTED]: What happens if you visualise the trajectory? Two orders of magnitude in scale of lipid movement should stick out like a sore thumb. - Original Message From: Justin A. Lemkul [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Wednesday, January 16, 2008 12:27:45 AM Subject: [gmx-users] About g_msd Hello again, I'm back with a few more questions about g_msd (version 3.3, in case I hadn't mentioned that before). Thanks to Xavier's message earlier, I have abandoned use of ordered trajectories to analyze my lipids. I will deal with lipid shells in the future. For now I am approaching the problem of lateral diffusion coefficients from a slightly different angle. My system contains a helical peptide that is oriented asymmetrically with respect to the DPPC bilayer. It is tilted and only partially embedded into the intracellular leaflet of the bilayer (at the beginning of the simulation). Due to the asymmetry, I would like to study the properties of the leaflets separately, including, among other parameters, the lateral diffusion coefficients of the component lipids. I have found a few papers that have simulated pure DPPC bilayers, and am using them as somewhat of a reference point for the magnitude of the lateral diffusion coefficients that I am determining: E. Lindahl and O. Edholm (2001) J. Chem. Phys. 115 (10), and U. Essmann and M. L. Berkowitz (1999) Biophys. J. 76. For the top leaflet of my bilayer, I am getting a value of D = (4.0+/-2.2)x10^-7 cm^2/sec (reasonable, in terms of order of magnitude, I think), but for the bottom leaflet, I am getting roughly (355.7+/-551.5)x10^-7 cm^2/sec. I figured this enormous number was due to artefacts of PBC, so I tried every iteration of trjconv -pbc, but to no avail. Every result is quite similar. I tried starting g_msd at a later time (10 ns, 25 ns) to determine if any large initial movements of lipids were responsible for the result, but I'm still coming up with the enormous value of D (albeit slightly lower, ~200+/-400) I am using g_msd -mol, with an index file that contains molecule numbers, and then using g_analyze on the output .xvg file to get the values of D. Has anyone ever experienced anything similar? Am I missing something obvious? Thanks in advance, as always, especially if you read the entirety of my lengthy message. -Justin Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (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 Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the
Re: [gmx-users] fatal errors in parallel but not on single processor
Patricia Francis-Lyon wrote: The same .top, .gro, .mdp and .tpr files are used on both single processor and parallel runs, with the GROMOS96 53a6 force field. Any help you can offer is much appreciated! Your symptoms are perplexing, but if you really managed to use the same .tpr files, then that might be the problem. You need to define the number of processes in the grompp command line that generates the .tpr file. Mark ___ 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] About g_msd (and noise)
Alan Dodd wrote: I've been playing with g_msd myself recently, and been seeing weird results toward the end of the simulation. From the below post, it looks like I was doing it correctly (apart from analysing the leaflets separately). Previous posts in the mailing list have implied that increased noise towards the end of a simulation is inherent in the algorithm, I just wanted to check that I was interpreting those posts correctly? And if this is so, do people just not show the results towards the end? DESCRIPTION --- g_msd computes the mean square displacement (MSD) of atoms from their initial positions. This provides an easy way to compute the diffusion constant using the Einstein relation. The time between additional starting points for the MSD calculation is set with -trestart. The diffusion constant is calculated by least squares fitting a straight line through the MSD from -beginfit to -endfit. An error estimate given, which is the difference of the diffusion coefficients obtained from fits over the two halfs of the fit interval. Have you tried these option? - Original Message From: David van der Spoel [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, January 16, 2008 6:48:32 AM Subject: Re: [gmx-users] About g_msd Justin A. Lemkul wrote: Hi Alan, Thanks for the reply. My initial trajectory showed several of the lipids jumped across the box and continued through the bilayer from there, which resulted in a large displacement, so I processed the trajectory with trjconv -pbc nojump. There is still a rather large initial displacement (within the first several nanoseconds out of 100, likely due to my equilibration procedure of packing the lipids tightly around the peptide), so I attempted to analyze the last 75 ns and 90 ns of the trajectory, using the structures at those times as the reference (in g_msd -s). Still the same result, a large value of D. Any ideas? please go back to your original trajectory and do normal g_msd for the P atoms only. (no mol flags etc.) Thanks again. -Justin Quoting Alan Dodd [EMAIL PROTECTED]: What happens if you visualise the trajectory? Two orders of magnitude in scale of lipid movement should stick out like a sore thumb. - Original Message From: Justin A. Lemkul [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Wednesday, January 16, 2008 12:27:45 AM Subject: [gmx-users] About g_msd Hello again, I'm back with a few more questions about g_msd (version 3.3, in case I hadn't mentioned that before). Thanks to Xavier's message earlier, I have abandoned use of ordered trajectories to analyze my lipids. I will deal with lipid shells in the future. For now I am approaching the problem of lateral diffusion coefficients from a slightly different angle. My system contains a helical peptide that is oriented asymmetrically with respect to the DPPC bilayer. It is tilted and only partially embedded into the intracellular leaflet of the bilayer (at the beginning of the simulation). Due to the asymmetry, I would like to study the properties of the leaflets separately, including, among other parameters, the lateral diffusion coefficients of the component lipids. I have found a few papers that have simulated pure DPPC bilayers, and am using them as somewhat of a reference point for the magnitude of the lateral diffusion coefficients that I am determining: E. Lindahl and O. Edholm (2001) J. Chem. Phys. 115 (10), and U. Essmann and M. L. Berkowitz (1999) Biophys. J. 76. For the top leaflet of my bilayer, I am getting a value of D = (4.0+/-2.2)x10^-7 cm^2/sec (reasonable, in terms of order of magnitude, I think), but for the bottom leaflet, I am getting roughly (355.7+/-551.5)x10^-7 cm^2/sec. I figured this enormous number was due to artefacts of PBC, so I tried every iteration of trjconv -pbc, but to no avail. Every result is quite similar. I tried starting g_msd at a later time (10 ns, 25 ns) to determine if any large initial movements of lipids were responsible for the result, but I'm still coming up with the enormous value of D (albeit slightly lower, ~200+/-400) I am using g_msd -mol, with an index file that contains molecule numbers, and then using g_analyze on the output .xvg file to get the values of D. Has anyone ever experienced anything similar? Am I missing something obvious? Thanks in advance, as always, especially if you read the entirety of my lengthy message. -Justin Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (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
Re: [gmx-users] About g_msd (and noise)
Hi Alan, see Fig 3 in the paper I was mentionning in my previous post (http://dx.doi.org/10.1063/1.2393240); from the legend the authors say 'deviation from linearity at long times is due to poor statistics'. So to answer your question, that's probably true, most papers just show the beginning of the plot where the MSD is linear. As quoted before by David, one has just to take care about fitting in the linear region (with the -beginfit and -endfit flags). Cheers, Patrick Alan Dodd a écrit : I've been playing with g_msd myself recently, and been seeing weird results toward the end of the simulation. From the below post, it looks like I was doing it correctly (apart from analysing the leaflets separately). Previous posts in the mailing list have implied that increased noise towards the end of a simulation is inherent in the algorithm, I just wanted to check that I was interpreting those posts correctly? And if this is so, do people just not show the results towards the end? - Original Message From: David van der Spoel [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, January 16, 2008 6:48:32 AM Subject: Re: [gmx-users] About g_msd Justin A. Lemkul wrote: Hi Alan, Thanks for the reply. My initial trajectory showed several of the lipids jumped across the box and continued through the bilayer from there, which resulted in a large displacement, so I processed the trajectory with trjconv -pbc nojump. There is still a rather large initial displacement (within the first several nanoseconds out of 100, likely due to my equilibration procedure of packing the lipids tightly around the peptide), so I attempted to analyze the last 75 ns and 90 ns of the trajectory, using the structures at those times as the reference (in g_msd -s). Still the same result, a large value of D. Any ideas? please go back to your original trajectory and do normal g_msd for the P atoms only. (no mol flags etc.) Thanks again. -Justin Quoting Alan Dodd [EMAIL PROTECTED]: What happens if you visualise the trajectory? Two orders of magnitude in scale of lipid movement should stick out like a sore thumb. - Original Message From: Justin A. Lemkul [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Wednesday, January 16, 2008 12:27:45 AM Subject: [gmx-users] About g_msd Hello again, I'm back with a few more questions about g_msd (version 3.3, in case I hadn't mentioned that before). Thanks to Xavier's message earlier, I have abandoned use of ordered trajectories to analyze my lipids. I will deal with lipid shells in the future. For now I am approaching the problem of lateral diffusion coefficients from a slightly different angle. My system contains a helical peptide that is oriented asymmetrically with respect to the DPPC bilayer. It is tilted and only partially embedded into the intracellular leaflet of the bilayer (at the beginning of the simulation). Due to the asymmetry, I would like to study the properties of the leaflets separately, including, among other parameters, the lateral diffusion coefficients of the component lipids. I have found a few papers that have simulated pure DPPC bilayers, and am using them as somewhat of a reference point for the magnitude of the lateral diffusion coefficients that I am determining: E. Lindahl and O. Edholm (2001) J. Chem. Phys. 115 (10), and U. Essmann and M. L. Berkowitz (1999) Biophys. J. 76. For the top leaflet of my bilayer, I am getting a value of D = (4.0+/-2.2)x10^-7 cm^2/sec (reasonable, in terms of order of magnitude, I think), but for the bottom leaflet, I am getting roughly (355.7+/-551.5)x10^-7 cm^2/sec. I figured this enormous number was due to artefacts of PBC, so I tried every iteration of trjconv -pbc, but to no avail. Every result is quite similar. I tried starting g_msd at a later time (10 ns, 25 ns) to determine if any large initial movements of lipids were responsible for the result, but I'm still coming up with the enormous value of D (albeit slightly lower, ~200+/-400) I am using g_msd -mol, with an index file that contains molecule numbers, and then using g_analyze on the output .xvg file to get the values of D. Has anyone ever experienced anything similar? Am I missing something obvious? Thanks in advance, as always, especially if you read the entirety of my lengthy message. -Justin Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (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
Re: [gmx-users] image control
Hi Myunggi Yi, In addition, it may help if you give some examples: link the structure file, the topology file, and some sample images highlighting the point your trying to make. Apparently, leaving us guessing doesn't help. Tsjerk On Jan 16, 2008 12:10 AM, Mark Abraham [EMAIL PROTECTED] wrote: Myunggi Yi wrote: Thank you. I know general setup to run a simulation, and I'm running one. As you see the title, I have problem with image. Well that was a dozen emails ago and we've talked about many topics since. You'll get nowhere fast by assuming that the people you're asking for help have the whole email exchange memorized... they have their own problems. To get effective help, describe things fully, and if you need to refer back to something, go and get a URL to the mailing list archives on the GROMACS webpage. This may seem onerous, but you're the one trying to get free help, so you maximise your chances by making life easier on the people who might give it to you. I'm getting broken lipid in the trajectory. You're not. mdrun doesn't write broken molecules if they were whole in the topology. Your visual representation might have them crossing PBC boundaries in a way that might make them look broken, however. There are many ways to adjust your visual representation, however. Would you let me know how to avoid this? As someone else has already suggested, judicious use of trjconv and the .gro file you use with VMD are needed here. Read the man page for trjconv and experiment to find what works for whatever your trying to do. Do I need special setup? No Mark ___ 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 -- 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://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] interchain bond
Thank you Xavier, but I still have problems because when I use merge, pdb2gmx doesn't want that the second peptide has NH3+ and COO- as terminals and doesn't understand if I use -ter when I am using -merge, so doesn't create the top file. What do you exactly mean for the numbering of atoms is important? I tried in two ways: 1. Each peptide starts form one 2. The second peptide numbering starts from the end of the first in both cases I have the same results and none of them works. Cheers and thank you, Velia Xavier Periole ha scritto: On Tue, 15 Jan 2008 16:32:54 +0100 Velia Minicozzi [EMAIL PROTECTED] wrote: Dear gromacs users, I have two identical peptides which should bind one metal ion. I guess I have not understood how I can make this bond. I labeled the two peptides with different chain identifier otherwise pdb2gmx does not understand that they are two peptides and not one protein. The metal is labeled with a third identifier, and I modified the ffoplsaabon.itp file inserting this bond and the specbond.dat file. Having 3 chains I have 3 different itp files and one top file in which all of the itp are called. Unfortunately in none of the itp files nor in the top file there is any reference to this bond I created, and after some time of MD simulation two of the atoms bound to the metal fly away even if I use constraints on all bonds. You have to use the merge option of pdb2gmx, it will generate one topology of the two peptides and the metal. Then you can add the bond within this topology file. The numbering of the atoms is important. If you create a chemical bond between two topologies (peptide-metal) this will not work. I guess I didn't create those bonds correctly. How should I do? Any help is welcome! Best, Velia ___ 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 NMR Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ 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] About g_msd
Quoting David van der Spoel [EMAIL PROTECTED]: Justin A. Lemkul wrote: Hi Alan, Thanks for the reply. My initial trajectory showed several of the lipids jumped across the box and continued through the bilayer from there, which resulted in a large displacement, so I processed the trajectory with trjconv -pbc nojump. There is still a rather large initial displacement (within the first several nanoseconds out of 100, likely due to my equilibration procedure of packing the lipids tightly around the peptide), so I attempted to analyze the last 75 ns and 90 ns of the trajectory, using the structures at those times as the reference (in g_msd -s). Still the same result, a large value of D. Any ideas? please go back to your original trajectory and do normal g_msd for the P atoms only. (no mol flags etc.) Thank you! This appears to be giving me reasonable results. I have several dozen more trajectories to analyze, and will report back if anything goes amiss, but so far it's a good start! -Justin Thanks again. -Justin Quoting Alan Dodd [EMAIL PROTECTED]: What happens if you visualise the trajectory? Two orders of magnitude in scale of lipid movement should stick out like a sore thumb. - Original Message From: Justin A. Lemkul [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Wednesday, January 16, 2008 12:27:45 AM Subject: [gmx-users] About g_msd Hello again, I'm back with a few more questions about g_msd (version 3.3, in case I hadn't mentioned that before). Thanks to Xavier's message earlier, I have abandoned use of ordered trajectories to analyze my lipids. I will deal with lipid shells in the future. For now I am approaching the problem of lateral diffusion coefficients from a slightly different angle. My system contains a helical peptide that is oriented asymmetrically with respect to the DPPC bilayer. It is tilted and only partially embedded into the intracellular leaflet of the bilayer (at the beginning of the simulation). Due to the asymmetry, I would like to study the properties of the leaflets separately, including, among other parameters, the lateral diffusion coefficients of the component lipids. I have found a few papers that have simulated pure DPPC bilayers, and am using them as somewhat of a reference point for the magnitude of the lateral diffusion coefficients that I am determining: E. Lindahl and O. Edholm (2001) J. Chem. Phys. 115 (10), and U. Essmann and M. L. Berkowitz (1999) Biophys. J. 76. For the top leaflet of my bilayer, I am getting a value of D = (4.0+/-2.2)x10^-7 cm^2/sec (reasonable, in terms of order of magnitude, I think), but for the bottom leaflet, I am getting roughly (355.7+/-551.5)x10^-7 cm^2/sec. I figured this enormous number was due to artefacts of PBC, so I tried every iteration of trjconv -pbc, but to no avail. Every result is quite similar. I tried starting g_msd at a later time (10 ns, 25 ns) to determine if any large initial movements of lipids were responsible for the result, but I'm still coming up with the enormous value of D (albeit slightly lower, ~200+/-400) I am using g_msd -mol, with an index file that contains molecule numbers, and then using g_analyze on the output .xvg file to get the values of D. Has anyone ever experienced anything similar? Am I missing something obvious? Thanks in advance, as always, especially if you read the entirety of my lengthy message. -Justin Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (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 Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs ___ 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
Re: [gmx-users] About g_msd
Patrick, Thanks for pointing this paper out. I'll have a look at it. As for now, I'm following David's advice and will see where that takes me. -Justin Quoting Patrick Fuchs [EMAIL PROTECTED]: Hi Justin, Wohlert and Edholm (http://dx.doi.org/10.1063/1.2393240) suggested to extract the motion of the 2 monolayers relative to each other, before calculating the MSD. This is an artefact coming from the finite size of computer simulations. This may explain the discrepancy you get between both leaflets. Second, they showed that there are two different diffusions. A fast diffusion occuring on ps time scale and a longer one which is brownian and can be compared to FRAP experiments. In their paper, they propose a fitting procedure that extracts both diffusion constants. Furthermore, be sure to equilibrate enough (a few tens of ns) before doing this analysis. Cheers, Patrick Justin A. Lemkul a écrit : Hi Alan, Thanks for the reply. My initial trajectory showed several of the lipids jumped across the box and continued through the bilayer from there, which resulted in a large displacement, so I processed the trajectory with trjconv -pbc nojump. There is still a rather large initial displacement (within the first several nanoseconds out of 100, likely due to my equilibration procedure of packing the lipids tightly around the peptide), so I attempted to analyze the last 75 ns and 90 ns of the trajectory, using the structures at those times as the reference (in g_msd -s). Still the same result, a large value of D. Any ideas? Thanks again. -Justin Quoting Alan Dodd [EMAIL PROTECTED]: What happens if you visualise the trajectory? Two orders of magnitude in scale of lipid movement should stick out like a sore thumb. - Original Message From: Justin A. Lemkul [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Wednesday, January 16, 2008 12:27:45 AM Subject: [gmx-users] About g_msd Hello again, I'm back with a few more questions about g_msd (version 3.3, in case I hadn't mentioned that before). Thanks to Xavier's message earlier, I have abandoned use of ordered trajectories to analyze my lipids. I will deal with lipid shells in the future. For now I am approaching the problem of lateral diffusion coefficients from a slightly different angle. My system contains a helical peptide that is oriented asymmetrically with respect to the DPPC bilayer. It is tilted and only partially embedded into the intracellular leaflet of the bilayer (at the beginning of the simulation). Due to the asymmetry, I would like to study the properties of the leaflets separately, including, among other parameters, the lateral diffusion coefficients of the component lipids. I have found a few papers that have simulated pure DPPC bilayers, and am using them as somewhat of a reference point for the magnitude of the lateral diffusion coefficients that I am determining: E. Lindahl and O. Edholm (2001) J. Chem. Phys. 115 (10), and U. Essmann and M. L. Berkowitz (1999) Biophys. J. 76. For the top leaflet of my bilayer, I am getting a value of D = (4.0+/-2.2)x10^-7 cm^2/sec (reasonable, in terms of order of magnitude, I think), but for the bottom leaflet, I am getting roughly (355.7+/-551.5)x10^-7 cm^2/sec. I figured this enormous number was due to artefacts of PBC, so I tried every iteration of trjconv -pbc, but to no avail. Every result is quite similar. I tried starting g_msd at a later time (10 ns, 25 ns) to determine if any large initial movements of lipids were responsible for the result, but I'm still coming up with the enormous value of D (albeit slightly lower, ~200+/-400) I am using g_msd -mol, with an index file that contains molecule numbers, and then using g_analyze on the output .xvg file to get the values of D. Has anyone ever experienced anything similar? Am I missing something obvious? Thanks in advance, as always, especially if you read the entirety of my lengthy message. -Justin Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (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 Never miss a thing. Make Yahoo your home page.
Re: [gmx-users] about parallel run
I decided to recompile mdrun with mpi support again and restart the simulation again. I also checked for lam running on the nodes and it was still running nevertheless I tried to halt lam. Now everything seems to be running ok. On Tue, 2008-01-15 at 12:24 -0500, [EMAIL PROTECTED] wrote: What i was trying to do is to run a parallel simulation. I have successfully compiled mdrun with mpi support. This is my grompp command grompp -f md.mdp -c rec_pr.gro -p rec.top -o rec.tpr -np 12 And this is the script I sent to the cluster: #!/bin/bash cd /home/yunierkis/MD export LAMRSH=ssh -x lamboot -v .nodes nohup mpirun -np 12 mdrun_mpi -s rec_md.tpr -o rec_md.trr -c rec_md.gro -e rec.edr -g rec_md.log -nice 0 -np 12 Are you sure that you are running Lam correctly on your machine? I would personally run it like this: /tools/lam/lam-7.1.2/bin/mpirun C mdrun_mpi -np 12 -deffnm rec_md I have deleted all #md.trr.*# files and the simulation is still running on all the 6 nodes and no new #md.trr.*# file have been created. It sounds very strange for me and I can't find an explanation. Did you have other #files# ? e.g. the .edr or .log ? Do you lamhalt properly after previous attempts? Yunierkis On Tue, 2008-01-15 at 11:54 +1100, Mark Abraham wrote: Yunierkis Perez Castillo wrote: Hi all, I'm new to gromacs. I have setup a protein MD simulation in a cluster, I'm using 6 computers with 2 CPUs each one. After gromacs begun running I had 12 trajectory files in the folder the output is written: md.trr #md.trr.1# #md.trr.2# #md.trr.11# It seems like the trajectory is replicated by each CPU the simulation is running on. All files has the same size, and grows simultaneously as the simulation advances. Is that a normal thing?? Can I delete the #* files?? I infer from your results that you've run 12 single-processor simulations from the same working directory. GROMACS makes backups of files when you direct it to write to an existing file, and these are numbered as #filename.index#. Your 12 simulations are all there, but you can't assume that those files with number 5 are all from the same simulation, because of the possibility of filesystem asynchronicities in creating the files. If you're trying to run 12 single-processor simulations in the same working directory, then you need to rethink your strategy. If you're trying to do something else, then you also need to rethink :-) Mark ___ 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 __ Servicio de Correos del Grupo de Redes. UCLV - Universidad 2008 del 11 al 15 de febrero del 2008. Palacio de Convenciones. La Habana. Cuba. http: //www.universidad2008.cu - II Taller internacional -Virtualizaci�n en la Educaci�n Superior-, del 11 al 15 de febrero de 2008 Palacio de Convenciones. La Habana, Cuba. http://virtual-es.uclv.edu.cu ___ 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] image control
I have tried to attach my .gro file, but it is not allowed in mailing list. I'm attaching small file of the snap shot of the gro file. The limit is 50 KB. What can I do? I'm attaching the file to you (Tsjerk Wassenaar). Again I didn't do any modification. This is a just output from MD. As you know you can check the coordinate in the .gro text file. This is not a visulalization problem. If any body wants, I will send you my .gro file. I downloaded popc.itp form Dr. Tieleman's web. As you see the lipid can be broken any bond (see two fragment of lipid at the bottom), however the left sile lipid are Okay. Any idea? On Jan 16, 2008 7:47 AM, Tsjerk Wassenaar [EMAIL PROTECTED] wrote: Hi Myunggi Yi, In addition, it may help if you give some examples: link the structure file, the topology file, and some sample images highlighting the point your trying to make. Apparently, leaving us guessing doesn't help. Tsjerk On Jan 16, 2008 12:10 AM, Mark Abraham [EMAIL PROTECTED] wrote: Myunggi Yi wrote: Thank you. I know general setup to run a simulation, and I'm running one. As you see the title, I have problem with image. Well that was a dozen emails ago and we've talked about many topics since. You'll get nowhere fast by assuming that the people you're asking for help have the whole email exchange memorized... they have their own problems. To get effective help, describe things fully, and if you need to refer back to something, go and get a URL to the mailing list archives on the GROMACS webpage. This may seem onerous, but you're the one trying to get free help, so you maximise your chances by making life easier on the people who might give it to you. I'm getting broken lipid in the trajectory. You're not. mdrun doesn't write broken molecules if they were whole in the topology. Your visual representation might have them crossing PBC boundaries in a way that might make them look broken, however. There are many ways to adjust your visual representation, however. Would you let me know how to avoid this? As someone else has already suggested, judicious use of trjconv and the .gro file you use with VMD are needed here. Read the man page for trjconv and experiment to find what works for whatever your trying to do. Do I need special setup? No Mark ___ gmx-users mailing list gmx-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 -- 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://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 ___ 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] how to perform a minimization of an isolated drug
Dear folks, I apologize in advance for asking a question which might have been already answered by the list. What I need is to do an energy minimization of an isolated drug using GROMACS. I found out from a previous message that it is possibe to do using the PRODRG server, but I wonder if it possible to do with GROMACS. Does anyone know how to do it ? Thanks a lot Sergio -- Sérgio de Alencar, M.Sc Bioinformatics PhD Student Universidade Federal de Minas Gerais, Brazil ___ 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] how to perform a minimization of an isolated drug
Quoting Sergio de Alencar [EMAIL PROTECTED]: Dear folks, I apologize in advance for asking a question which might have been already answered by the list. What I need is to do an energy minimization of an isolated drug using GROMACS. I found out from a previous message that it is possibe to do using the PRODRG server, but I wonder if it possible to do with GROMACS. Does anyone know how to do it ? Just like you would anything else. Use the coordinates and topology from PRODRG (beware that the charges are likely unsatisfactory, and ffgmx is deprecated!) as input into grompp with an appropriate .mdp file for minimization. -Justin Thanks a lot Sergio -- Sérgio de Alencar, M.Sc Bioinformatics PhD Student Universidade Federal de Minas Gerais, Brazil Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (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
[gmx-users] Re: Go-model Hamiltonian (Xavier Periole)
Hello. In the website server, I provide my email, some workid and submit the pdb file. A window appears, in which it says: *Go model built. Email will be sent to [EMAIL PROTECTED] Thank you for using MMTSB Web Services. *I have tried many different emails, but I dont get any thing in the email. Eduardo I was planning to use CHARMM but I found a problem at a server that builds the respective Go-model Hamiltonian from a pdb file I do not know anybody who as used a Go-model in GMX but it should not be so difficult using tabulated potentials! this is the website in case you are interested: http://mmtsb.scripps.edu/webservices/gomodel.html What is wrong with the website server? Does it give a wrong topology? We have been using it for a peptide and that would be nice if you could detail the bug. ___ 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] position restraint on a plane
Dear users, How can I restrain a certain atoms on a plane? For example, I want to restrain phosphurus atoms of lipid molecules at z=1.0nm. Is there a way to do this? -- 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 ___ 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] position restraint on a plane
Myunggi Yi wrote: Dear users, How can I restrain a certain atoms on a plane? For example, I want to restrain phosphurus atoms of lipid molecules at z=1.0 nm. Is there a way to do this? You can either freeze in one dimension or position restrain to a plane, by setting the force constants appropriately. In that case the atom will go out of the plane however. -- 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 ___ 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 -- David van der Spoel, Ph.D. 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
Re: [gmx-users] position restraint on a plane
Thank you. I'm a beginner. How can I setup the restrain? Where should I get the information. The manual is not enough for me. The position restraint .itp file dosen't seem to offer for the reference (z= 1.0) option. Whould give me more detail? On Jan 16, 2008 3:14 PM, David van der Spoel [EMAIL PROTECTED] wrote: Myunggi Yi wrote: Dear users, How can I restrain a certain atoms on a plane? For example, I want to restrain phosphurus atoms of lipid molecules at z=1.0 nm. Is there a way to do this? You can either freeze in one dimension or position restrain to a plane, by setting the force constants appropriately. In that case the atom will go out of the plane however. -- 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 ___ 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 -- David van der Spoel, Ph.D. 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 -- 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 ___ 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] position restraint on a plane
check http://wiki.gromacs.org/index.php/Position_Restraints ___ 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] position restraint on a plane
Where should I put z=1.0 ? On Jan 16, 2008 3:22 PM, Anirban Mudi [EMAIL PROTECTED] wrote: check http://wiki.gromacs.org/index.php/Position_Restraints ___ 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 ___ 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] Re: Go-model Hamiltonian (Xavier Periole)
On Wed, 16 Jan 2008 13:07:27 -0600 eddie mendel [EMAIL PROTECTED] wrote: Hello. In the website server, I provide my email, some workid and submit the pdb file. A window appears, in which it says: *Go model built. Email will be sent to [EMAIL PROTECTED] Thank you for using MMTSB Web Services. *I have tried many different emails, but I dont get any thing in the email. That might be due to many things. Did you contact them to find out what the problem is? I am sure they would appreciate the info. XAvier Eduardo I was planning to use CHARMM but I found a problem at a server that builds the respective Go-model Hamiltonian from a pdb file I do not know anybody who as used a Go-model in GMX but it should not be so difficult using tabulated potentials! this is the website in case you are interested: http://mmtsb.scripps.edu/webservices/gomodel.html What is wrong with the website server? Does it give a wrong topology? We have been using it for a peptide and that would be nice if you could detail the bug. ___ 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 NMR Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ 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] position restraint on a plane
Thank you. I've already read the part, but I was wondering how can I supply my reference z positon in the .itp file. I can prepare the restraint.gro file manually by placing the atoms at z= 1.0 nm. Then I think I can supply with -r option. Have a great day. On Jan 16, 2008 3:44 PM, Mark Abraham [EMAIL PROTECTED] wrote: Myunggi Yi wrote: Thank you. I'm a beginner. How can I setup the restrain? Where should I get the information. The manual is not enough for me. There's even an example of planar restraints in chapter 5. The position restraint .itp file dosen't seem to offer for the reference (z= 1.0) option. Whould give me more detail? You're not constraining to a plane, you're restraining the coordinates to be near the plane it starts on (but for advanced usage read about grompp -r). For now, see the links on the URL that Anirban provided. Mark ___ 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 ___ 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] position restraint on a plane
Quoting Myunggi Yi [EMAIL PROTECTED]: Thank you. I've already read the part, but I was wondering how can I supply my reference z positon in the .itp file. You don't. If you read the link that was provided earlier, or the manual, as has been suggested, you will find that posre.itp does not contain coordinate information; it supplies force constant information. Again, refer here: http://wiki.gromacs.org/index.php/Position_Restraints -Justin I can prepare the restraint.gro file manually by placing the atoms at z= 1.0 nm. Then I think I can supply with -r option. Have a great day. On Jan 16, 2008 3:44 PM, Mark Abraham [EMAIL PROTECTED] wrote: Myunggi Yi wrote: Thank you. I'm a beginner. How can I setup the restrain? Where should I get the information. The manual is not enough for me. There's even an example of planar restraints in chapter 5. The position restraint .itp file dosen't seem to offer for the reference (z= 1.0) option. Whould give me more detail? You're not constraining to a plane, you're restraining the coordinates to be near the plane it starts on (but for advanced usage read about grompp -r). For now, see the links on the URL that Anirban provided. Mark ___ 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 Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (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] position restraint on a plane
On Wed, 16 Jan 2008 16:12:23 -0500 Justin A. Lemkul [EMAIL PROTECTED] wrote: Quoting Myunggi Yi [EMAIL PROTECTED]: Thank you. I've already read the part, but I was wondering how can I supply my reference z positon in the .itp file. There are no direct way to restrain an atom to stay a a particular value in one direction (in a plan). However the solution you propose could actually work. You might need to use small force constants at the beginning, all the atoms won't be in the plan in the reference structure and forcing them to move may be a problem. The posre.itp should contain the list of the atoms with the three (x,y,z) force constant you want to use. The details are indeed in the manual. good luck. You don't. If you read the link that was provided earlier, or the manual, as has been suggested, you will find that posre.itp does not contain coordinate information; it supplies force constant information. Again, refer here: http://wiki.gromacs.org/index.php/Position_Restraints -Justin I can prepare the restraint.gro file manually by placing the atoms at z= 1.0 nm. Then I think I can supply with -r option. Have a great day. On Jan 16, 2008 3:44 PM, Mark Abraham [EMAIL PROTECTED] wrote: Myunggi Yi wrote: Thank you. I'm a beginner. How can I setup the restrain? Where should I get the information. The manual is not enough for me. There's even an example of planar restraints in chapter 5. The position restraint .itp file dosen't seem to offer for the reference (z= 1.0) option. Whould give me more detail? You're not constraining to a plane, you're restraining the coordinates to be near the plane it starts on (but for advanced usage read about grompp -r). For now, see the links on the URL that Anirban provided. Mark ___ 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 Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (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 NMR Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ 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] interchain bond
On Wed, 16 Jan 2008 22:29:31 +0100 (CET) Velia Minicozzi [EMAIL PROTECTED] wrote: Hi Xavier, I think it works I just deleted the 3 H at the N-terminus of the second chain and when I used merge in pdb2gmx it worked! Thanks a lot! Cool. What I meant with the atom numbers is that now you can open your gro file and look for the atom numbers to bound and go to the itp file and add a bond (in the [ bond ]section) using these atom numbers. Previously grompp would have attributed then to the same molecule. Now they should be bound. You can check the tpr file using gmxdump -s topol.tpr Velia On Tue, January 15, 2008 8:50 pm, Xavier Periole said: On Tue, 15 Jan 2008 16:32:54 +0100 Velia Minicozzi [EMAIL PROTECTED] wrote: Dear gromacs users, I have two identical peptides which should bind one metal ion. I guess I have not understood how I can make this bond. I labeled the two peptides with different chain identifier otherwise pdb2gmx does not understand that they are two peptides and not one protein. The metal is labeled with a third identifier, and I modified the ffoplsaabon.itp file inserting this bond and the specbond.dat file. Having 3 chains I have 3 different itp files and one top file in which all of the itp are called. Unfortunately in none of the itp files nor in the top file there is any reference to this bond I created, and after some time of MD simulation two of the atoms bound to the metal fly away even if I use constraints on all bonds. You have to use the merge option of pdb2gmx, it will generate one topology of the two peptides and the metal. Then you can add the bond within this topology file. The numbering of the atoms is important. If you create a chemical bond between two topologies (peptide-metal) this will not work. I guess I didn't create those bonds correctly. How should I do? Any help is welcome! Best, Velia ___ 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 NMR Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - * Velia Minicozzi Department of Physics University of Rome Tor Vergata Via della Ricerca Scientifica, 1 00133 Rome - Italy tel. +39 06 72594554 fax. +39 06 2023507 http://biophys.roma2.infn.it/ * ___ 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 NMR Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ 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] FEP trajectory errors
Hello everyone, I'm computing the free energy of binding of a DNA base on a carbon nanotube. I think it's a pretty simple calculation and I'm proceeding in a very standard way. This is what I'm doing: I have the optimal orientation of the base on the nanotube. I'm constraining the positions of the base atoms with a soft harmonic potential. I then am running two different FEP calculations: one where I turn off the charges on the base atoms and a second where I then turn off all the lennard-jones parameters for the base atoms. For each of these I use the following: delta_lambda = 0 sc_alpha = 0.7 sc_power = 1 sc_sigma = 0.3 I run a series of trajectories at constant lambda values from 0 to 1. However, I notice some problems with the trajectories when I turn off the LJ parameters. As lambda is varied from 0 to 1, it seems that the position restraints no longer are being applied. Additionally, the DNA base geometry starts to become severely distorted at lambda values greater than about 0.6. This happens despite the fact that I am not perturbing the internal bonded interactions of the base. Here is a sample of my topology (included just the first line of each section): [ moleculetype ] ; Namenrexcl dg-disappear 3 [ atoms ] 1 P 1 DG P 1 1.1659 30.9700 DUM 0. 30.9700 ... [ bonds ] 1 2 1 0.1480 439320. 0.1480 439320. ... [ angles ] 1 4 5 1 120.5001836.8000 120.5001836.8000 ... [ dihedrals ] 1 4 5 8 1 0. 1.6039 3 0. 1.6039 3 ... [ position_restraints ] 1 1 100 100 100 100 100 100 ... So you can see that I am not perturbing the bonded interactions as I have just copied the same values from topology A. Also, I am experiencing additional problems when lambda=1. After about 2ns, all the motion in the system begins to freeze and all the atoms simply vibrate about a fixed position. Soon after that the simulation crashes. Can anyone comment on what's going on here? Thanks, Bob Johnson ___ 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] MPI issue
I am running gromacs on a machine with altivec support. My understanding is I have to use MVAPICH on this machine. I occasionally have runs crash and I receive the following error n559(0): Loaded with Money n536(14): 14 - MPI_ALLREDUCE : Null communicator n536(14): [14] [] Aborting Program! n559(0): 0 - MPI_ALLREDUCE : Null communicator n559(0): [0] [] Aborting Program! Cleaning up all processes ...Cleaning up all processes ...done. Does this indicate a problem with the machine, mvapich, or gromacs? Again, this doesn't always happen, just sometimes (which makes me suspect it is a machine issue). Any advice on where the problem might be would be helpful. thanks in advance. -Paul ___ 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] MPI issue
Paul Whitford wrote: I am running gromacs on a machine with altivec support. My understanding is I have to use MVAPICH on this machine. There is no coupling between altivec and MPI varirant. I occasionally have runs crash and I receive the following error n559(0): Loaded with Money n536(14): 14 - MPI_ALLREDUCE : Null communicator n536(14): [14] [] Aborting Program! n559(0): 0 - MPI_ALLREDUCE : Null communicator n559(0): [0] [] Aborting Program! Cleaning up all processes ...Cleaning up all processes ...done. Does this indicate a problem with the machine, mvapich, or gromacs? Again, this doesn't always happen, just sometimes (which makes me suspect it is a machine issue). Any advice on where the problem might be would be helpful. thanks in advance. If it is reproducible it could be MPI or GROMACS. I use openmpi, and sometimes when I abort a job the next one will not start, but the one after, due to some leftovers somewhere on the system. Unless this is reproducible it is impossible to debug, otherwise it could even be flaky hardware. -Paul ___ 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 -- David van der Spoel, Ph.D. 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
Re: [gmx-users] MPI issue
Hi Paul, is this version 3.3.1? If I am not missing something, the only two instances where MPI_Allreduce could be used are in pme.c and in network.c, but the respective parts of the code have to be explicitly switched on by a preprocessor directive. Anyway, the communicator on which they operate is MPI_COMM_WORLD and this should never be NULL. Or does the error happen at the very end of the simulations? Then maybe it's a problem with MPI_Finalize (you might want to have a look at gmx_finalize in network.c then). If you are using the CVS version things are different, because Allreduce is used more often. Is there additional information in the error report that tells in which routine the problem occurs? Carsten Paul Whitford wrote: I am running gromacs on a machine with altivec support. My understanding is I have to use MVAPICH on this machine. I occasionally have runs crash and I receive the following error n559(0): Loaded with Money n536(14): 14 - MPI_ALLREDUCE : Null communicator n536(14): [14] [] Aborting Program! n559(0): 0 - MPI_ALLREDUCE : Null communicator n559(0): [0] [] Aborting Program! Cleaning up all processes ...Cleaning up all processes ...done. Does this indicate a problem with the machine, mvapich, or gromacs? Again, this doesn't always happen, just sometimes (which makes me suspect it is a machine issue). Any advice on where the problem might be would be helpful. thanks in advance. -Paul ___ 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. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Department Am Fassberg 11 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/research/dep/grubmueller/ http://www.gwdg.de/~ckutzne ___ 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
