Re: [gmx-users] Gibbs free energy of binding
Dear Gromacs users I want to calculate Gibbs free energy too,but about Protein-drug binding. Please guide more clearly,what texts I need to read for learning how can I do it? Besides,g-energy has an option for estimating free energy from trajectory file(-fee option) I thought if I had a trajectory file of binding state I could estimate binding free energy by this option. am I right? does it give me Gibbs free energy?(Is this equall to binding free energy?) thanks in advance Mohsen On Tue, Oct 19, 2010 at 2:56 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahab shariati wrote: Hi gromacs users Can I use gromacs for obtaining Gibbs free energy of binding of protein and dna? Yes. I would suggest you read about potential of mean force calculations. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_dipole ? = what is the bond length of the ionic bond in the dipole moment calculation?
On 2010-10-20 06.06, Chih-Ying Lin wrote: Hi molecule dipole is 48.0 sum of q_i x_i x_i the bond length for covalent bond. No. x_i is the atomic position. but what is x_i for salt-molecule? For salt-molecule, the ionic bonds are broken in water solvent and the counter ions are spread among the water. What is the x_i of the ionic bond in the dipole moment calculation? Is x_i equal to the distance of the two parts of the salt-molecules (the counter ion and the rest of the molecule) even though the salt molecule has dissolved in the water? I mean, is x_i equal to the length of simulation box if the counter ion and the rest of the molecule are in the two sides of the simulation box? I mean, if Gromacs takes x_i as the length of simulation box if the counter ion and the rest of the molecule are in the two sides of the simulation box? Thank you Lin Try http://en.wikipedia.org/wiki/Electric_dipole_moment , you might want to read the part about calculating dipole moments for an array of point charges, it is not difficult. 33 point charges are doable using pencil and calculator in about 10min. Do not worry about the reference point as long as your system is neutral, just set it to (0,0,0). Otherwise, take any kind of first year physics book it will contain very similar information. On 10/19/2010 05:39 AM, Chih-Ying Lin wrote: Hi According to the following website, http://en.wikipedia.org/wiki/Bond_dipole_moment \mu = \delta \, d. The bond dipole is modeled as +ä -- ä- with a distance /d/ between the partial charges http://en.wikipedia.org/wiki/Partial_charges +ä and ä-. For a complete molecule the total molecular dipole moment may be approximated as the vector sum of individual bond dipole moments. However, for a molecule of multiple atoms, There may be more than one bond connected on one atom. E | B - A - C partial charge of atom_A = -0.5 partial charge of atom_B = 0.2 partial charge of atom_C = 0.35 partial charge of atom_E = 0.4 Which partial charges should I use when I calculate bond-dipole-moment of A-B ? Which partial charges should I use when I calculate bond-dipole-moment of A-C ? Which partial charges should I use when I calculate bond-dipole-moment of A-E ? Thank you Lin On 2010-10-18 03.30, Chih-Ying Lin wrote: HI I confined one molecule in the center of box and issue the g_dipole command. The average dipole moment is still around 32. It is the molecule with 33 atoms / united atoms of most carbon groups, isn't the dipole moment around 32 too high? How can I test next and know that the dipole moment around 32 is acceptable? By calculating on paper: dipole is 48.0 sum of q_i x_i, therefore if you have large charge separation you will get a large dipole. Thank you Lin On 2010-10-16 21.36, Chih-Ying Lin wrote: Hi I issue the g_dipole command on Gromacs = And, the following information is shown. There are 10 molecules in the selection, Does the Average =32.1611 refer to the average for a single over the simulation time? Or, the Average = 32.1611 summing for all the 10 molecules over the simulation time? If the average = 32.1611 for a single molecule with 33 atoms / united atoms of most carbon groups, isn't the dipole moment too high? I think this is the average per molecule. You may need to run trjconv -pbc whole, because mdrun may break molecules in two parts, meaning that the molecule becomes as big as the box. What does will subtract their charge at their center of mass this mean? Why will subtract their charge at their center of mass ? -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20101019/4cf32833/attachment.html -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0.
Alright.. I actually simulated my protein for 5ns. Then I loaded the trajectory file and .gro file in vmd. Then, I extracted one of the frame and write it into pdb format, When I open it with vmd, one of the atom from a residue is connected to another atom in another residue. Things like this happens as VMD uses a distance-based bond determination heuristic. Therefore, I would need a structure file which specifies the bonds for my structure so that VMD doesn't have to guess. So how can I generate the structure file I needed? Thanks. Regards, Joyce From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Wednesday, October 20, 2010 2:25:26 Subject: Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0. Kwee Hong wrote: I executed the script at the therminal by typing perl top2psf.pl -i topol.top -o zz.psf Here, I attached my input file. Your topology does not correspond to a MARTINI coarse-grained topology. As such, probably a bunch of the pattern matching is getting incorrect information. You cannot use top2psf.pl with this type of topology. It was created for a very specific purpose and requires that format, nothing else. -Justin *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wednesday, October 20, 2010 2:14:34 *Subject:* Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0. Kwee Hong wrote: Hi, I've got a top2psf.pl script from the web and used it to generate a psf file. Yet it generated some bonds to atoms with index 0 which should not occur. It causes VMD cannot load it and had a segmentation fault. vmd Info) Using plugin psf for structure file /home/birg/Desktop/zz.psf ERROR) Error reading bond information. Segmentation fault I wonder am I getting the right top2psf.pl. Or is there any place I can get the latest stable version of that script? There is only one version. Zeros are only printed if something goes wrong, i.e. you have provided the wrong input or something else has failed. Based solely on the information you've provided I cannot diagnose what has gone wrong. -Justin Here, I attached the perl script I used. Thanks. Regards, Joyce -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error on install Gromacs 4
On Oct 20, 2010, at 5:17 AM, Son Tung Ngo wrote: Dear experts, I have just install gromacs 4.5.1 on my cluster (using CentOS that was install openmpi1.5, Platform MPI, fftw3, g77, gcc , g++) but I have problem with size of int : [r...@icstcluster gromacs-4.5.1]# ./configure --prefix=/shared/apps/gromacs --enable-mpi --enable-double snip checking for _aligned_malloc... no checking size of int... 0 checking size of long int... 0 checking size of long long int... 0 checking size of off_t... configure: error: in `/shared/apps/source/gromacs-4.5.1': configure: error: cannot compute sizeof (off_t) Any idea about this? Hi Son, search the config.log file for your error message cannot compute sizeof (off_t). There you can find some more explanation. Could be a missing library. Carsten-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Template file in gromacs4.5.1
On Tue, Oct 19, 2010 at 4:14 PM, Sikandar Mashayak symasha...@gmail.com wrote: Now I have upgraded to gromacs4.5.1 and when I check its template file , its completely different that the earlier version. Does that mean old post-processing codes have to rewritten if I were to use new gromacs? No, it does not. Some function parameters have changed, and you will need to make small changes to your post-processing codes to make them compile with 4.5.1, but all the old functionality is still there. However, if you want to take advantage of the new selection functionality in 4.5 and make your post-processing tools much more powerful, you will need to use the new template. On Wed, Oct 20, 2010 at 00:40, Sikandar Mashayak symasha...@gmail.com wrote: Also, will there be any errors if I use trajectory computed by gromacs4.5.1 and use post processing code developed for gromacs4.0.7. If you change your tools to make them compile against 4.5.1, they should work just fine. If you use the ones compiled for 4.0.7, they should be able to read a trajectory from 4.5.1 without problems, but they can't read .tpr files from 4.5.1, so in practice you may run into problems. - Teemu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] -pbc nojump
On 20/10/2010 9:07 PM, leila karami wrote: Hi gromacs users I study simulation of protein-dna interaction using gromacs. After full md simulation, because of diffusion of one strand of dna to edge of box, I used trjconv -f old.xtc –o new.xtc –s *.tpr -pbc nojump -ur compact –center. By this way my first problem is solved. 1)Should I use new xtc file for analysis section? That depends what you want to observe, and whether periodicity is relevant to that observation. 2)When I see new xtc file, there isn’t any water molecule in interface between protein and dna(where as there were water molecules interface between protein and dna, before full md simulation). I want to survey water mediated hydrogen bond between protein and dna. Do –pbc nojump cause to this problem? Probably. Probably what you want is to center on the combined protein+DNA group (need to make an index group) and then put the COM of all residues in the box. That will mean your water region and surrounds of interest are contiguous. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] -pbc nojump
Dear Mark thanks for your attention when I used trjconv -pbc nojump, I made one group (protein and dna) in index file and I selected that as centering group. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] -pbc nojump
On 20/10/2010 9:24 PM, leila karami wrote: Dear Mark thanks for your attention when I used trjconv -pbc nojump, I made one group (protein and dna) in index file and I selected that as centering group. What is the problem? :-) You might need two passes with trjconv. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] -pbc nojump
Dear Mark my mean of [when I used trjconv -pbc nojump, I made one group (protein and dna) in index file and I selected that as centering group.] is that the problem (nonentity of water molecules in interface of protein and dna) was not solved. what is your mean of [You might need two passes with trjconv]? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fwd: [gmx-users] Hardware-specific crash with 4.5.1
Please keep all Gromacs-related correspondence on the gmx-users list, and do not hijack an old, unrelated thread to ask questions. I am CC'ing the list and I would ask that all further discussion take place there. I have no answer to your question, aside from advising you to read the primary literature for the force fields for which implicit solvent parameters were derived. -Justin weixin wrote: Hi, Justin, Where to get those parameters for GB simulation which should be put in the top file: [ implicit_genborn_params ] Thanks, weixin -- Forwarded message -- From: *Justin A. Lemkul* jalem...@vt.edu mailto:jalem...@vt.edu Date: 2010/9/27 Subject: [gmx-users] Hardware-specific crash with 4.5.1 To: Gromacs Users' List gmx-users@gromacs.org mailto:gmx-users@gromacs.org Hi All, I'm hoping I might get some tips in tracking down the source of an issue that appears to be hardware-specific, leading to crashes in my system. The failures are occurring on our supercomputer (Mac OSX 10.3, PowerPC). Running the same .tpr file on my laptop (Mac OSX 10.5.8, Intel Core2Duo) and on another workstation (Ubuntu 10.04, AMD64) produce identical results. I suspect the problem stems from unsuccessful energy minimization, which then leads to a crash when running full MD. All jobs were run in parallel on two cores. The supercomputer does not support threading, so MPI is invoked using MPICH-1.2.5 (native MPI implementation on the cluster). Details as follows: EM md.log file: successful run (Intel Core2Duo or AMD64) Steepest Descents converged to Fmax 1000 in 7 steps Potential Energy = -4.8878180e+04 Maximum force = 8.7791553e+02 on atom 5440 Norm of force = 1.1781271e+02 EM md.log file: unsuccessful run (PowerPC) Steepest Descents converged to Fmax 1000 in 1 steps Potential Energy = -2.4873273e+04 Maximum force = 0.000e+00 on atom 0 Norm of force =nan MD invoked from the minimized structure generated on my laptop or AMD64 runs successfully (at least for a few hundred steps in my test), but the MD on the PowerPC cluster fails immediately: Step Time Lambda 00.00.0 Energies (kJ/mol) U-BProper Dih. Improper Dih. CMAP Dih.GB Polarization 7.93559e+039.34958e+032.24036e+02 -2.47750e+03 -7.83599e+04 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Potential 7.70042e+039.94520e+04 -1.17168e+04 -5.79783e+04 -2.55780e+04 Kinetic En. Total EnergyTemperature Pressure (bar) Constr. rmsd nannannan0.0e+00nan Constr.2 rmsd nan DD step 9 load imb.: force 3.0% --- Program mdrun_4.5.1_mpi, VERSION 4.5.1 Source code file: nsgrid.c, line: 601 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ind has value 7131. It should have been within [ 0 .. 7131 ] For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- It seems as if the crash really shouldn't be happening, if the value range is inclusive. Running with all-vs-all kernels works, but the performance is horrendously slow (300 ps per day for a 7131-atom system) so I am attempting to use long cutoffs (2.0 nm) as others on the list have suggested. Details of the installations and .mdp files are appended below. -Justin === em.mdp === ; Run parameters integrator = steep ; EM emstep = 0.005 emtol = 1000 nsteps = 5 nstcomm = 1 comm_mode = angular ; non-periodic system ; Bond parameters constraint_algorithm= lincs constraints = all-bonds continuation= no; starting up ; required cutoffs for implicit nstlist = 1 ns_type = grid rlist = 2.0 rcoulomb= 2.0 rvdw= 2.0 ; cutoffs required for qq and vdw coulombtype = cut-off vdwtype = cut-off ; temperature coupling tcoupl = no ; Pressure coupling is off Pcoupl = no ; Periodic boundary conditions are off for implicit pbc = no ; Settings for implicit solvent implicit_solvent= GBSA gb_algorithm= OBC rgbradii= 2.0 === md.mdp === ; Run parameters integrator = sd; velocity Langevin
Re: [gmx-users] -pbc nojump
On 20/10/2010 9:55 PM, leila karami wrote: Dear Mark my mean of [when I used trjconv -pbc nojump, I made one group (protein and dna) in index file and I selected that as centering group.] is that the problem (nonentity of water molecules in interface of protein and dna) was not solved. what is your mean of [You might need two passes with trjconv]? You might need to use trjconv once to center, and then again to put all the molecules in the box (or similar). trjconv can't always do everything you want in one invocation. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gibbs free energy of binding
mohsen ramezanpour wrote: Dear Gromacs users I want to calculate Gibbs free energy too,but about Protein-drug binding. Please guide more clearly,what texts I need to read for learning how can I do it? Look into the literature and nearly any of the popular simulation textbooks. Besides,g-energy has an option for estimating free energy from trajectory file(-fee option) I thought if I had a trajectory file of binding state I could estimate binding free energy by this option. am I right? does it give me Gibbs free energy?(Is this equall to binding free energy?) Never used this option, but from the description of the option, it calculates delta(G) relative to an ideal gas state, which sounds completely unrelated to what you want to accomplish. Besides, if g_energy could magically solve this difficult problem, no one would bother with more thorough methods, like PMF or thermodynamic integration. -Justin thanks in advance Mohsen On Tue, Oct 19, 2010 at 2:56 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahab shariati wrote: Hi gromacs users Can I use gromacs for obtaining Gibbs free energy of binding of protein and dna? Yes. I would suggest you read about potential of mean force calculations. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0.
Kwee Hong wrote: Alright.. I actually simulated my protein for 5ns. Then I loaded the trajectory file and .gro file in vmd. Then, I extracted one of the frame and write it into pdb format, When I open it with vmd, one of the atom from a residue is connected to another atom in another residue. Things like this happens as VMD uses a distance-based bond determination heuristic. Therefore, I would need a structure file which specifies the bonds for my structure so that VMD doesn't have to guess. So how can I generate the structure file I needed? I've never tried it myself, but editconf purports to write CONECT records when it extracts a structure from a .tpr file. You could construct a .tpr using the desired frame, then try to convert it to a .pdb file with CONECT records. Other than that, there may be some VMD tricks to get it to work, but I can't comment there. -Justin Thanks. Regards, Joyce *From:* Justin A. Lemkul jalem...@vt.edu *To:* Gromacs Users' List gmx-users@gromacs.org *Sent:* Wednesday, October 20, 2010 2:25:26 *Subject:* Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0. Kwee Hong wrote: I executed the script at the therminal by typing perl top2psf.pl -i topol.top -o zz.psf Here, I attached my input file. Your topology does not correspond to a MARTINI coarse-grained topology. As such, probably a bunch of the pattern matching is getting incorrect information. You cannot use top2psf.pl with this type of topology. It was created for a very specific purpose and requires that format, nothing else. -Justin *From:* Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Wednesday, October 20, 2010 2:14:34 *Subject:* Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0. Kwee Hong wrote: Hi, I've got a top2psf.pl script from the web and used it to generate a psf file. Yet it generated some bonds to atoms with index 0 which should not occur. It causes VMD cannot load it and had a segmentation fault. vmd Info) Using plugin psf for structure file /home/birg/Desktop/zz.psf ERROR) Error reading bond information. Segmentation fault I wonder am I getting the right top2psf.pl. Or is there any place I can get the latest stable version of that script? There is only one version. Zeros are only printed if something goes wrong, i.e. you have provided the wrong input or something else has failed. Based solely on the information you've provided I cannot diagnose what has gone wrong. -Justin Here, I attached the perl script I used. Thanks. Regards, Joyce -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list
[gmx-users] -pbc nojump
Dear Mark you said in answer to -pbc nojump that using of new xtc file for analysis section depends what one wants to observe. what observations is relevant to periodicity? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gibbs free energy of binding
Dear Justin You are right,But I searched in tools and I found g_sham It is very useful tool for estimating Gibbs free energy,Enthalepy , emtropy and ... I think I can use from that for my calculation of binding free energy(In the other words,del G free energy of system ) how do you think about g_sham? On Wed, Oct 20, 2010 at 2:28 PM, Justin A. Lemkul jalem...@vt.edu wrote: mohsen ramezanpour wrote: Dear Gromacs users I want to calculate Gibbs free energy too,but about Protein-drug binding. Please guide more clearly,what texts I need to read for learning how can I do it? Look into the literature and nearly any of the popular simulation textbooks. Besides,g-energy has an option for estimating free energy from trajectory file(-fee option) I thought if I had a trajectory file of binding state I could estimate binding free energy by this option. am I right? does it give me Gibbs free energy?(Is this equall to binding free energy?) Never used this option, but from the description of the option, it calculates delta(G) relative to an ideal gas state, which sounds completely unrelated to what you want to accomplish. Besides, if g_energy could magically solve this difficult problem, no one would bother with more thorough methods, like PMF or thermodynamic integration. -Justin thanks in advance Mohsen On Tue, Oct 19, 2010 at 2:56 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: shahab shariati wrote: Hi gromacs users Can I use gromacs for obtaining Gibbs free energy of binding of protein and dna? Yes. I would suggest you read about potential of mean force calculations. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gibbs free energy of binding
mohsen ramezanpour wrote: Dear Justin You are right,But I searched in tools and I found g_sham It is very useful tool for estimating Gibbs free energy,Enthalepy , emtropy and ... I think I can use from that for my calculation of binding free energy(In the other words,del G free energy of system ) how do you think about g_sham? It is not applicable. g_sham simply determines free energies based on histograms of two independent variables. PMF is the appropriate technique for what you want to do. I can see no other effective way to conduct your study using Gromacs. -Justin On Wed, Oct 20, 2010 at 2:28 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: mohsen ramezanpour wrote: Dear Gromacs users I want to calculate Gibbs free energy too,but about Protein-drug binding. Please guide more clearly,what texts I need to read for learning how can I do it? Look into the literature and nearly any of the popular simulation textbooks. Besides,g-energy has an option for estimating free energy from trajectory file(-fee option) I thought if I had a trajectory file of binding state I could estimate binding free energy by this option. am I right? does it give me Gibbs free energy?(Is this equall to binding free energy?) Never used this option, but from the description of the option, it calculates delta(G) relative to an ideal gas state, which sounds completely unrelated to what you want to accomplish. Besides, if g_energy could magically solve this difficult problem, no one would bother with more thorough methods, like PMF or thermodynamic integration. -Justin thanks in advance Mohsen On Tue, Oct 19, 2010 at 2:56 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahab shariati wrote: Hi gromacs users Can I use gromacs for obtaining Gibbs free energy of binding of protein and dna? Yes. I would suggest you read about potential of mean force calculations. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read
Re: [gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)
vinothkumar mohanakrishnan wrote: Hi Justin I corrected the mistake what you said and i am able to run energy minimisation and equilibration. but when i view my em.gro and equilibration.gro in VMD it seems to me that the bonds between the atoms are broken in molecules.I used g_energy to check weather the system has VMD tries to guess where bonds should be, but does not always do a good job. Your topology defines bonds. These are the only bonds that there will be. None can be broken or formed in standard MD. equilibrated to the required temperature (300K) i found that the variation in the temperature was 100K (plus r minus) . i am not able find out what went wrong. any help is highly appreciated. Without seeing your .mdp file, there's no way to know. The fluctuation does seem too high, though, unless your system really is just that unstable. Are other properties converged - potential energy, density, etc? What type of ensemble are you using? -Justin Regards Vinoth On Mon, Oct 18, 2010 at 6:09 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: vinothkumar mohanakrishnan wrote: Dear Justin what corrections i should make to ffoplsaan.itp to make it correct. what i should give instead of CAB and CLAA?. You must use atom types, not names. Unfortunately, you've chosen to use atom names, which are also types, which makes all of this quite confusing if you're not sure what you're doing. You defined two new atom types - opls_966 (CAB) and opls_967 (CLAA), which are the only indicators you are allowed to use if introducing new types. Thus, references to atom names (CAC, CLAD) will generate fatal errors. i copied the .rtp .atp .itp files from usr/local/gromacs/share/gromacs/top to my working directory and added these parameters to the corresponding files. what you mean is should i need to add these parameters to the source directory ( usr/local/gromacs/share/gromacs/top)? Your topology needs to be consistent with whatever files need to be included. By default, Gromacs checks the working directory first, but if you've moved to a new (sub)directory to carry out further steps, the grompp will not find your modified files, but will instead locate only the default force field files in $GMXLIB. Either keep all your work in one directory (which can get messy), or make use of the include keyword in the .mdp file. Any directory specified there will be searched after the working directory, but before $GMXLIB. -Justin Regards Vinoth On Mon, Oct 18, 2010 at 5:27 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: vinothkumar mohanakrishnan wrote: Hi all i added new atomtype for dichloroethane (DCE) and added the corresponding parameters in the .rtp, .atp, .bon.itp, .nb.itp respectively. given below are my additions to the corresponding files respectively. *ffoplsaa.rtp* [ DCE ] [ atoms ] CLAA opls_967 -0.2270 1 CAB opls_966 0.2270 1 CAC opls_966 0.2270 2 CLAD opls_967 -0.2270 2 [ bonds ] CLAACAB CABCAC CACCLAD [ angles ] CLAACABCAC CABCACCLAD [ dihedrals ] CLAACABCACCLAD *ffoplsaa.atp* opls_966 14.02700 ; CH2 for DCE opls_967 35.45300 ; CL for DCE *ffoplsaabon.itp* [bondtypes] CLAA CAB 10.17870 194137.6 ; CL-CH2 for DCE CAB CAC 10.15300 259408.0 ; CH2-CH2 for DCE CAC CLAD10.17870 194137.6 ; CL-CH2 for DCE [angletypes] CLAA CAB CAC 1 108.200368.192 ; C-C-CL for DCE CAB CAC CLAD 1 108.200368.192 ; C-C-CL for DCE [dihedraltypes] CLAA CAB CAC CLAD 3 20.76096 -0.4184 27.011904 0.0 0.0 0.0 ; for DCE You shouldn't be using atom names in the [*types] directives. What you should be using are the interpolated types from ffoplsaanb.itp, thus you have only utilized opls_966 (CAB) and opls_967 (CLAA). *ffoplsaanb.itp* opls_966 CAB614.027000.227 A 3.98000e-01 4.76976e-01 ; CH2 of DCE opls_967 CLAA 17 35.45300 -0.227 A 3.16000e-01
[gmx-users] Force-field files location and order of reading in Gromacs 4.5.2
Hi all, I have detected that preference in reading forcefield files in Gromacs 4.5 has probably been changed from Gromacs 4.0.x and older. In older gromacs, when there was forcefield with modification present in my working directory, then it was read preferentially, but now it seems that forcefield is primarily read from /share/top directory - Am I right? In 4.5.2 I have tried to have modified gromos53a6.ff in my working directory, but the modification was not used by gromacs. The only way around was to rename the files in any of these manners: 1) directory to gromos53a6b.ff and forcefield.itp therein to have include gromos53a6b.ff/ffnonbonded.itp and gromos53a6b.ff/ffbonded.itp and point md.top to gromos53a6b.ff/forcefield.itp or 2) simply copy all files from ff directory to root and mention them in md.top (forcefield.itp has to be changed afterwards) However both of these modifications are rather messy. -- Zdraví skoro zdravý Karel Krápník Berka RNDr. Karel Berka, Ph.D. Palacký University in Olomouc Faculty of Science Department of Physical Chemistry tř. 17. listopadu 1192/12 771 46 Olomouc tel: +420-585634769 fax: +420-585634769 e-mail: karel.be...@upol.cz -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Force-field files location and order of reading in Gromacs 4.5.2
Karel Berka wrote: Hi all, I have detected that preference in reading forcefield files in Gromacs 4.5 has probably been changed from Gromacs 4.0.x and older. In older gromacs, when there was forcefield with modification present in my working directory, then it was read preferentially, but now it seems that forcefield is primarily read from /share/top directory - Am I right? The working directory is still searched first. In 4.5.2 I have tried to have modified gromos53a6.ff in my working directory, but the modification was not used by gromacs. What do you mean not used? Was the wrong force field called when using pdb2gmx? Gromacs prints a list of force field subdirectories in the working directory, then in GMXLIB, and allows you to choose. In the 4.5.x series, you need a full working subdirectory of the modified force field. The only way around was to rename the files in any of these manners: 1) directory to gromos53a6b.ff and forcefield.itp therein to have include gromos53a6b.ff/ffnonbonded.itp and gromos53a6b.ff/ffbonded.itp and point md.top to gromos53a6b.ff/forcefield.itp This should not be necessary. or 2) simply copy all files from ff directory to root and mention them in md.top (forcefield.itp has to be changed afterwards) Copying all the files from the desired *.ff subdirectory into the working directory (of whatever name you choose) is a correct procedure. There should be no need to manually modify the .top file, unless you're somehow manually generating it, as well. With pdb2gmx, the modified files can be read like any other force field. -Justin However both of these modifications are rather messy. -- Zdraví skoro zdravý Karel Krápník Berka RNDr. Karel Berka, Ph.D. Palacký University in Olomouc Faculty of Science Department of Physical Chemistry tř. 17. listopadu 1192/12 771 46 Olomouc tel: +420-585634769 fax: +420-585634769 e-mail: karel.be...@upol.cz mailto:karel.be...@upol.cz -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] -pbc nojump
On 20/10/2010 10:26 PM, shahab shariati wrote: Dear Mark you said in answer to -pbc nojump that using of new xtc file for analysis section depends what one wants to observe. what observations is relevant to periodicity? Anything that measures where something is relative to another. Normally one is only interested in the nearest periodic image. IIRC, some of the GROMACS tools are PBC-aware and determine the nearest suitable for themselves, other times they treat the trajectory as if there were no periodicity. In the latter case, if your results will be sensitive to the actual locations of atoms with respect to the periodic cell, then you'll wish to use trjconv to choose the configuration best suited to your needs. In the analysis desired the original post, the waters should all be in the same cell as the DNA+protein interstice, hence centering the cell on that group, and putting all waters into the cell. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Gromacs build error
Hello, I am trying to build Gromacs 4.5 from source using the Portland Group compiler: [r...@master1 gromacs-4.5]# echo $CPPFLAGS -I/cvos/shared/apps/fftw/pgi/64/3.1.2/include [r...@master1 gromacs-4.5]# echo $LDFLAGS -L/cvos/shared/apps/fftw/pgi/64/3.1.2/lib [r...@master1 gromacs-4.5]# echo $CC /cvos/shared/apps/pgi/7.0.7/linux86-64/7.0/bin/pgcc [r...@master1 gromacs-4.5]# [r...@master1 gromacs-4.5]# ./configure --enable-shared --enable-double --enable-mpi --prefix=/cvos/apps/gromacs-4.5 --program-suffix=_mpi_d [ see output below ] However, when I try to build Gromacs, I get the following error which looks to be a syntax error in the code: [r...@master1 gromacs-4.5]# make [ ... lots of output ... ] mpicc -DHAVE_CONFIG_H -I. -I../../../../src -I/usr/include/libxml2 -I../../../../include -DGMXLIBDIR=\/cvos/apps/gromacs-4.5/share/top\ -I/cvos/shared/apps/fftw/pgi/64/3.1.2/include -fast -pc 32 -c nb_kernel400_x86_64_sse2.c -DPIC -o .libs/nb_kernel400_x86_64_sse2.o PGC-S-0080-Missing braces for array, structure, or union initialization (../../../../include/gmx_sse2_double.h: 457) PGC-S-0094-Illegal type conversion required (../../../../include/gmx_sse2_double.h: 514) PGC-S-0094-Illegal type conversion required (../../../../include/gmx_sse2_double.h: 515) PGC-S-0094-Illegal type conversion required (../../../../include/gmx_sse2_double.h: 516) PGC-S-0094-Illegal type conversion required (../../../../include/gmx_sse2_double.h: 517) PGC/x86-64 Linux 7.0-7: compilation completed with severe errors make[5]: *** [nb_kernel400_x86_64_sse2.lo] Error 1 make[5]: Leaving directory `/gpfs/ueasystem/escluster/gromacs-4.5/src/gmxlib/nonbonded/nb_kernel_x86_64_sse2' make[4]: *** [all-recursive] Error 1 make[4]: Leaving directory `/gpfs/ueasystem/escluster/gromacs-4.5/src/gmxlib/nonbonded' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/gpfs/ueasystem/escluster/gromacs-4.5/src/gmxlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/gpfs/ueasystem/escluster/gromacs-4.5/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/gpfs/ueasystem/escluster/gromacs-4.5/src' make: *** [all-recursive] Error 1 [r...@master1 gromacs-4.5]# Any help will be greatly appreciated. --- configure output checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... no checking whether /cvos/shared/apps/pgi/7.0.7/linux86-64/7.0/bin/pgcc accepts -g... yes checking for /cvos/shared/apps/pgi/7.0.7/linux86-64/7.0/bin/pgcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of /cvos/shared/apps/pgi/7.0.7/linux86-64/7.0/bin/pgcc... none checking dependency style of /cvos/shared/apps/pgi/7.0.7/linux86-64/7.0/bin/pgcc... none checking for mpxlc... no checking for mpicc... mpicc checking whether the MPI cc command works... yes checking for MPI_IN_PLACE in collective operations... no checking for catamount... no checking how to run the C preprocessor... mpicc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether ln -s works... yes checking whether mpicc accepts -fast -pc 32... yes checking whether byte ordering is bigendian... no checking that size_t can hold pointers... yes checking for SIGUSR1... yes checking for pipes... yes checking floating-point format... IEEE754 (little-endian byte and word order) checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /bin/sed checking for non-GNU ld... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking whether we are using the GNU C++ compiler... no checking whether mpicc accepts -g... no checking dependency style of mpicc... none checking how to run the C++ preprocessor... /lib/cpp checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from mpicc object... failed checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking
Re: [gmx-users] Gromacs build error
Hi, I am trying to build Gromacs 4.5 from source using the Portland Group compiler: Have you tried adding -Mm128 to CFLAGS? A. -- Ansgar Esztermann DV-Systemadministration Max-Planck-Institut für biophysikalische Chemie, Abteilung 105 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Gromacs build error
Hello Ansgar, What does this switch do? When I do set the variable, it cannot even create the Makefiles: [r...@master1 gromacs-4.5]# ./configure --enable-shared --enable-double --enable-mpi --prefix=/cvos/apps/gromacs-4.5 --program-suffix=_mpi_d checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for C compiler default output file name... configure: error: in `/gpfs/ueasystem/escluster/gromacs-4.5': configure: error: C compiler cannot create executables See `config.log' for more details. [r...@master1 gromacs-4.5]# Thanks, Wadud. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Esztermann, Ansgar Sent: Wednesday, October 20, 2010 3:03 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Gromacs build error Hi, I am trying to build Gromacs 4.5 from source using the Portland Group compiler: Have you tried adding -Mm128 to CFLAGS? A. -- Ansgar Esztermann DV-Systemadministration Max-Planck-Institut für biophysikalische Chemie, Abteilung 105 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gromacs build error
Hi, What does this switch do? When I do set the variable, it cannot even create the Makefiles: According to the manpage, it enables the __m128 types. The original error message points to a line containing such a type. I've looked at the PGI 10.3 manpage -- other versions may behave differently. configure: error: in `/gpfs/ueasystem/escluster/gromacs-4.5': configure: error: C compiler cannot create executables See `config.log' for more details. Is there something useful in config.log? A. -- Ansgar Esztermann DV-Systemadministration Max-Planck-Institut für biophysikalische Chemie, Abteilung 105 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gromacs build error
On Wed, 2010-10-20 at 16:37 +0200, Esztermann, Ansgar wrote: Hi, What does this switch do? When I do set the variable, it cannot even create the Makefiles: According to the manpage, it enables the __m128 types. The original error message points to a line containing such a type. I've looked at the PGI 10.3 manpage -- other versions may behave differently. configure: error: in `/gpfs/ueasystem/escluster/gromacs-4.5': configure: error: C compiler cannot create executables See `config.log' for more details. I wouldn't bother trying to compile gromacs 4.5.1 with pgi 9 or later. They broke __m128 compatibility with gcc/intel/pathscale and have a bug in the compiler that triggers on the __m128 usage in gromacs 4.5.1. patschale 3.2 and older also fails to build this but the upcoming new 4.0 version (which i'm beta testing) builds fine. No benchmark results yet though. -- Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden Internet: a...@hpc2n.umu.se Phone: +46 90 7866134 Fax: +46 90 7866126 Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] FEP Calculation problem on GMX 4.5.1
Hello! I am new to this list, probably someone has have the same problem I am facing now with the use of Gromacs to calculate FEP (Free energy pertubaion). I've followed the gromacs tutorial for Free energy Calculation available at http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial, for lambda value ranging from 0 to 1 in 11 independent job for each lambda value. Unfortunately, the* dVpot/dlambda dEkin/dlambda dG/dl constr* values in the *.log are continuously coming zero. I Can use g_analyse, g_lie and g_energy but all results in zero. Does anyone has any idea on what is going on? Is there any tutorial for free energy calculation for Gromacs 4.5.1? Any help will be highly appreciated. My best regards Marcelo Brandão -- Marcelo Mendes Brandão Postdoc fellow Laboratório de Biologia Molecular de Plantas - ESALQ/USP Website: http://bioinfo.esalq.usp.br AtPIN: http://bioinfo.esalq.usp.br/atpin SKYPE: mmbrand Tel: (+55) 19 3429 4442 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] FEP Calculation problem on GMX 4.5.1
On October 20, 2010 at 9:22 PM Marcelo Brando brandao.marc...@gmail.com wrote: Hello! I am new to this list, probably someone has have the same problem I am facing now with the use of Gromacs to calculate FEP (Free energy pertubaion). Ive followed the gromacs tutorial for Free energy Calculation available at http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial, for lambda value ranging from 0 to 1 in 11 independent job for each lambda value. Unfortunately, the* dVpot/dlambda dEkin/dlambda dG/dl constr* values in the *.log are continuously coming zero. I did this but with gaff and amber03 ff and it worked out fine. I have no idea why you are getting dVpot/dLambda= 0. I would make sure you have all the settings set correctly. I Can use g_analyse, g_lie and g_energy but all results in zero. Does anyone has any idea on what is going on? Is there any tutorial for free energy calculation for Gromacs 4.5.1? Any help will be highly appreciated. My best regards Marcelo Brando -- Marcelo Mendes Brando Postdoc fellow Laboratrio de Biologia Molecular de Plantas - ESALQ/USP Website: http://bioinfo.esalq.usp.br AtPIN: http://bioinfo.esalq.usp.br/atpin SKYPE: mmbrand Tel: (+55) 19 3429 4442 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Cant post? Read http://www.gromacs.org/Support/Mailing_Lists TJ Mustard Email: musta...@onid.orst.edu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] FEP Calculation problem on GMX 4.5.1
TJ Mustard wrote: On October 20, 2010 at 9:22 PM Marcelo Brandão brandao.marc...@gmail.com wrote: Hello! I am new to this list, probably someone has have the same problem I am facing now with the use of Gromacs to calculate FEP (Free energy pertubaion). I've followed the gromacs tutorial for Free energy Calculation available at http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial, for lambda value ranging from 0 to 1 in 11 independent job for each lambda value. Unfortunately, the* dVpot/dlambda dEkin/dlambda dG/dl constr* values in the *.log are continuously coming zero. I did this but with gaff and amber03 ff and it worked out fine. I have no idea why you are getting dVpot/dLambda= 0. I would make sure you have all the settings set correctly. Posting an .mdp file would greatly improve the odds of getting this figured out. If you're getting all zeros, you probably aren't actually interpolating between the A and B states. Note that the free energy code underwent a major overhaul between version 3.3.3 and 4.0, so the tutorial linked above may not be entirely applicable any more. It is certainly useful in a general sense, but many of the .mdp settings have changed. -Justin I Can use g_analyse, g_lie and g_energy but all results in zero. Does anyone has any idea on what is going on? Is there any tutorial for free energy calculation for Gromacs 4.5.1? Any help will be highly appreciated. My best regards Marcelo Brandão -- Marcelo Mendes Brandão Postdoc fellow Laboratório de Biologia Molecular de Plantas - ESALQ/USP Website: http://bioinfo.esalq.usp.br AtPIN: http://bioinfo.esalq.usp.br/atpin SKYPE: mmbrand Tel: (+55) 19 3429 4442 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists TJ Mustard Email: musta...@onid.orst.edu -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] question about periodic boundary conditions
Hi, Is there a way to quantitatively determine, from a trajectory file, whether a molecule is interacting with a copy of itself in the adjacent box (given that PBC is applied)? Currently, I'm using VMD - I've already loaded the *xtc file into the*gro structure file and viewed the periodic images to draw under the Periodic tab of Graphical Representations. But I figure there's got to be an analytical way to do this, using g_dist or g_mindist? How the molecule is interacting (with its adjacent copy) is not the primary interest - I just want to know whether interactions among adjacent molecules are occurring. Does anyone have any ideas? Thanks, Lili -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] question about periodic boundary conditions
rainy...@yahoo.com wrote: Hi, Is there a way to quantitatively determine, from a trajectory file, whether a molecule is interacting with a copy of itself in the adjacent box (given that PBC is applied)? Currently, I'm using VMD - I've already loaded the *xtc file into the*gro structure file and viewed the periodic images to draw under the Periodic tab of Graphical Representations. But I figure there's got to be an analytical way to do this, using g_dist or g_mindist? How the molecule is interacting (with its adjacent copy) is not the primary interest - I just want to know whether interactions among adjacent molecules are occurring. From g_mindist -h: With option -pi the minimum distance of a group to its periodic image is plotted. This is useful for checking if a protein has seen its periodic image during a simulation. Only one shift in each direction is considered, giving a total of 26 shifts. It also plots the maximum distance within the group and the lengths of the three box vectors. -Justin Does anyone have any ideas? Thanks, Lili -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] question about periodic boundary conditions
rainy...@yahoo.com wrote: Hi Justin, Thanks for getting back to me. I executed the following command using g_mindist: $gromacs/g_mindist -pi -f n12_random_all.xtc -s n12_random.tpr -n index.ndx -od mindist.xvg ..and got the output (see below). It shows that the minimal distance to periodic image is at the most a few nm, but when I look in VMD, it is very apparent that there overlap between portions of the molecule. If so, wouldn't the minimal distance be negative? I've even executed the above command with the -pbc flag, and get the same output. I'm not sure how to interpret these results.Any additional feedback on your end would be greatly appreciated. Without context, I don't know how to interpret your results either. Do you have a single solute? Or multiple equivalent molecules? If you have a single solute, I think it's quite likely that your molecule of interest has seen its periodic image. You shouldn't be concerned with the largest value you see, you should be concerned with the smallest. Towards the end of your output, you've got values as low as ~0.55 nm. I'm assuming that you're using conventional cutoffs of no smaller than 1.0 nm or so, in which case you've very clearly violated the minimum image convention. This agrees with your observations using VMD. -Justin Thanks, Lili # Giant Rising Ordinary Mutants for A Clerical Setup # @title Minimum distance to periodic image @xaxis label Time (ps) @yaxis label Distance (nm) @TYPE xy @ subtitle and maximum internal distance @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend min per. @ s1 legend max int. @ s2 legend box1 @ s3 legend box2 @ s4 legend box3 04.226 22.198 20.402 8.824 15.015 500 3.475 21.944 19.423 8.400 14.296 1000 4.266 21.065 19.420 8.397 14.295 1500 3.934 21.430 19.421 8.396 14.297 2000 3.999 21.850 19.424 8.395 14.301 2500 4.031 20.793 19.426 8.394 14.303 3000 3.469 21.160 19.425 8.392 14.304 3500 3.902 21.372 19.425 8.390 14.305 4000 4.321 20.999 19.424 8.388 14.306 4500 4.667 19.447 19.428 8.388 14.310 5000 4.794 19.991 19.430 8.387 14.312 5500 4.909 19.142 19.430 8.384 14.313 6000 5.317 19.153 19.432 8.383 14.315 6500 5.110 19.223 19.431 8.381 14.315 7000 4.864 19.127 19.434 8.380 14.318 7500 4.246 18.680 19.438 8.380 14.322 8000 4.508 18.937 19.438 8.377 14.322 8500 4.441 17.865 19.440 8.376 14.324 9000 4.104 19.036 19.438 8.373 14.324 9500 4.676 18.528 19.439 8.371 14.325 14.313 18.953 19.443 8.371 14.328 105004.045 18.462 19.441 8.368 14.328 110005.013 19.162 19.443 8.367 14.330 115005.131 18.435 19.446 8.366 14.333 120005.054 17.814 19.447 8.364 14.335 125004.792 17.266 19.445 8.361 14.334 130003.684 16.897 19.451 8.361 14.339 135003.885 16.450 19.451 8.359 14.340 140004.007 17.088 19.453 8.357 14.342 145003.846 17.498 19.456 8.356 14.345 snip 172500 0.619 12.210 19.702 7.999 14.791 173000 0.668 12.609 19.703 8.000 14.793 173500 0.559 12.401 19.702 7.999 14.793 174000 0.507 12.638 19.701 8.000 14.794 174500 0.518 12.512 19.697 7.998 14.792 175000 0.757 12.316 19.701 8.000 14.796 175500 0.581 12.105 19.696 7.998 14.793 176000 0.810 11.777 19.696 7.999 14.794 176500 0.763 11.521 19.694 7.998 14.794 177000 0.666 11.886 19.697 7.999 14.797 177500 0.760 11.598 19.694 7.999 14.796 178000 0.495 11.356 19.689 7.997 14.793 178500 0.782 11.741 19.693 7.999 14.797 179000 0.509 11.908 19.692 7.999 14.798 179500 0.654 12.413 19.690 7.998 14.797 18 0.840 12.171 19.694 8.000 14.801 180500 0.631 12.090 19.690 7.999 14.800 181000 0.511 12.345 19.692 8.000 14.802 181500 0.494 12.205 19.688 7.999 14.801 182000 0.579 13.061 19.689 8.000 14.803 182500 0.496 13.220 19.687 7.999 14.803 snip 1.02e+06 0.785 13.881 19.555 7.999 14.902 1.0205e+06 0.920 13.526 19.552 7.998 14.900 1.021e+060.764 12.981 19.551 7.998 14.899 1.0215e+06 1.000 13.326 19.554 7.999 14.901 1.022e+060.983 13.016 19.552 7.998 14.899 1.0225e+06 0.969 13.209 19.553 7.999 14.900 1.023e+060.826 13.377 19.555 7.999 14.901 1.0235e+06 0.717 12.895 19.555 7.999 14.901 1.024e+060.868 13.191 19.555 7.999 14.902 1.0245e+06 0.868 12.682 19.557 8.000 14.903 1.025e+06
Re: [gmx-users] FEP Calculation problem on GMX 4.5.1
I would have this in my production mdp files, or something like it: ; Free energy control stuff free-energy = yes ; = no init-lambda = XXX ; = 0 delta-lambda = 0 ; = 0 foreign_lambda = ; = sc-alpha = 0.5 ; = 0 sc-power = 1.0 ; = 0 sc-sigma = 0.3 ; = 0.3 nstdhdl = 10 ; = 10 separate-dhdl-file = yes ; = yes dhdl-derivatives = yes ; = yes dh_hist_size = 0 ; = 0 dh_hist_spacing = 0.1 ; = 0.1 couple-moltype = methane ; = couple-lambda0 = vdw-q ; = vdw-q couple-lambda1 = none ; = vdw-q couple-intramol = no ; = no Changing XXX for your lambda values. Also make sure you name your couple-moltype correctly. If you use lig use lig for your couple-moltype. It will most likely fail if you set it up wrong. Also the manual explains these settings, so you can understand what they do. Thank you, TJ Mustard You can also find some info on the gmx-users mail log/forum by searching for FEP gromacs on google. It is somewhat hard to find but it can be found. On October 20, 2010 at 9:22 PM Marcelo Brando brandao.marc...@gmail.com wrote: Hello! I am new to this list, probably someone has have the same problem I am facing now with the use of Gromacs to calculate FEP (Free energy pertubaion). Ive followed the gromacs tutorial for Free energy Calculation available at http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial, for lambda value ranging from 0 to 1 in 11 independent job for each lambda value. Unfortunately, the* dVpot/dlambda dEkin/dlambda dG/dl constr* values in the *.log are continuously coming zero. I Can use g_analyse, g_lie and g_energy but all results in zero. Does anyone has any idea on what is going on? Is there any tutorial for free energy calculation for Gromacs 4.5.1? Any help will be highly appreciated. My best regards Marcelo Brando -- Marcelo Mendes Brando Postdoc fellow Laboratrio de Biologia Molecular de Plantas - ESALQ/USP Website: http://bioinfo.esalq.usp.br AtPIN: http://bioinfo.esalq.usp.br/atpin SKYPE: mmbrand Tel: (+55) 19 3429 4442 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Cant post? Read http://www.gromacs.org/Support/Mailing_Lists TJ Mustard Email: musta...@onid.orst.edu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] question about periodic boundary conditions
Justin, I have a single solute. But I understand what you're saying about the cutoff. My long-range cutoff is set to 1.2 nm (from MARTINI force field), so therefore, the snapshots corresponding to a minimum periodic distance of 1.2 nm would agree with the overlap witnessed in VMD? Thanks again, Lili On 20 October 2010 13:58, Justin A. Lemkul jalem...@vt.edu wrote: rainy...@yahoo.com wrote: Hi Justin, Thanks for getting back to me. I executed the following command using g_mindist: $gromacs/g_mindist -pi -f n12_random_all.xtc -s n12_random.tpr -n index.ndx -od mindist.xvg ..and got the output (see below). It shows that the minimal distance to periodic image is at the most a few nm, but when I look in VMD, it is very apparent that there overlap between portions of the molecule. If so, wouldn't the minimal distance be negative? I've even executed the above command with the -pbc flag, and get the same output. I'm not sure how to interpret these results.Any additional feedback on your end would be greatly appreciated. Without context, I don't know how to interpret your results either. Do you have a single solute? Or multiple equivalent molecules? If you have a single solute, I think it's quite likely that your molecule of interest has seen its periodic image. You shouldn't be concerned with the largest value you see, you should be concerned with the smallest. Towards the end of your output, you've got values as low as ~0.55 nm. I'm assuming that you're using conventional cutoffs of no smaller than 1.0 nm or so, in which case you've very clearly violated the minimum image convention. This agrees with your observations using VMD. -Justin Thanks, Lili # Giant Rising Ordinary Mutants for A Clerical Setup # @title Minimum distance to periodic image @xaxis label Time (ps) @yaxis label Distance (nm) @TYPE xy @ subtitle and maximum internal distance @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend min per. @ s1 legend max int. @ s2 legend box1 @ s3 legend box2 @ s4 legend box3 04.226 22.198 20.402 8.824 15.015 500 3.475 21.944 19.423 8.400 14.296 1000 4.266 21.065 19.420 8.397 14.295 1500 3.934 21.430 19.421 8.396 14.297 2000 3.999 21.850 19.424 8.395 14.301 2500 4.031 20.793 19.426 8.394 14.303 3000 3.469 21.160 19.425 8.392 14.304 3500 3.902 21.372 19.425 8.390 14.305 4000 4.321 20.999 19.424 8.388 14.306 4500 4.667 19.447 19.428 8.388 14.310 5000 4.794 19.991 19.430 8.387 14.312 5500 4.909 19.142 19.430 8.384 14.313 6000 5.317 19.153 19.432 8.383 14.315 6500 5.110 19.223 19.431 8.381 14.315 7000 4.864 19.127 19.434 8.380 14.318 7500 4.246 18.680 19.438 8.380 14.322 8000 4.508 18.937 19.438 8.377 14.322 8500 4.441 17.865 19.440 8.376 14.324 9000 4.104 19.036 19.438 8.373 14.324 9500 4.676 18.528 19.439 8.371 14.325 14.313 18.953 19.443 8.371 14.328 105004.045 18.462 19.441 8.368 14.328 110005.013 19.162 19.443 8.367 14.330 115005.131 18.435 19.446 8.366 14.333 120005.054 17.814 19.447 8.364 14.335 125004.792 17.266 19.445 8.361 14.334 130003.684 16.897 19.451 8.361 14.339 135003.885 16.450 19.451 8.359 14.340 140004.007 17.088 19.453 8.357 14.342 145003.846 17.498 19.456 8.356 14.345 snip 172500 0.619 12.210 19.702 7.999 14.791 173000 0.668 12.609 19.703 8.000 14.793 173500 0.559 12.401 19.702 7.999 14.793 174000 0.507 12.638 19.701 8.000 14.794 174500 0.518 12.512 19.697 7.998 14.792 175000 0.757 12.316 19.701 8.000 14.796 175500 0.581 12.105 19.696 7.998 14.793 176000 0.810 11.777 19.696 7.999 14.794 176500 0.763 11.521 19.694 7.998 14.794 177000 0.666 11.886 19.697 7.999 14.797 177500 0.760 11.598 19.694 7.999 14.796 178000 0.495 11.356 19.689 7.997 14.793 178500 0.782 11.741 19.693 7.999 14.797 179000 0.509 11.908 19.692 7.999 14.798 179500 0.654 12.413 19.690 7.998 14.797 18 0.840 12.171 19.694 8.000 14.801 180500 0.631 12.090 19.690 7.999 14.800 181000 0.511 12.345 19.692 8.000 14.802 181500 0.494 12.205 19.688 7.999 14.801 182000 0.579 13.061 19.689 8.000 14.803 182500 0.496 13.220 19.687 7.999 14.803 snip 1.02e+06 0.785 13.881 19.555 7.999 14.902 1.0205e+06 0.920 13.526 19.552 7.998 14.900 1.021e+060.764 12.981 19.551 7.998 14.899 1.0215e+06 1.000
Re: [gmx-users] question about periodic boundary conditions
rainy...@yahoo.com wrote: Justin, I have a single solute. But I understand what you're saying about the cutoff. My long-range cutoff is set to 1.2 nm (from MARTINI force field), so therefore, the snapshots corresponding to a minimum periodic distance of 1.2 nm would agree with the overlap witnessed in VMD? Indeed. You've violated the minimum image convention. -Justin Thanks again, Lili On 20 October 2010 13:58, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: rainy...@yahoo.com mailto:rainy...@yahoo.com wrote: Hi Justin, Thanks for getting back to me. I executed the following command using g_mindist: $gromacs/g_mindist -pi -f n12_random_all.xtc -s n12_random.tpr -n index.ndx -od mindist.xvg ..and got the output (see below). It shows that the minimal distance to periodic image is at the most a few nm, but when I look in VMD, it is very apparent that there overlap between portions of the molecule. If so, wouldn't the minimal distance be negative? I've even executed the above command with the -pbc flag, and get the same output. I'm not sure how to interpret these results.Any additional feedback on your end would be greatly appreciated. Without context, I don't know how to interpret your results either. Do you have a single solute? Or multiple equivalent molecules? If you have a single solute, I think it's quite likely that your molecule of interest has seen its periodic image. You shouldn't be concerned with the largest value you see, you should be concerned with the smallest. Towards the end of your output, you've got values as low as ~0.55 nm. I'm assuming that you're using conventional cutoffs of no smaller than 1.0 nm or so, in which case you've very clearly violated the minimum image convention. This agrees with your observations using VMD. -Justin Thanks, Lili # Giant Rising Ordinary Mutants for A Clerical Setup # @title Minimum distance to periodic image @xaxis label Time (ps) @yaxis label Distance (nm) @TYPE xy @ subtitle and maximum internal distance @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend min per. @ s1 legend max int. @ s2 legend box1 @ s3 legend box2 @ s4 legend box3 04.226 22.198 20.402 8.824 15.015 500 3.475 21.944 19.423 8.400 14.296 1000 4.266 21.065 19.420 8.397 14.295 1500 3.934 21.430 19.421 8.396 14.297 2000 3.999 21.850 19.424 8.395 14.301 2500 4.031 20.793 19.426 8.394 14.303 3000 3.469 21.160 19.425 8.392 14.304 3500 3.902 21.372 19.425 8.390 14.305 4000 4.321 20.999 19.424 8.388 14.306 4500 4.667 19.447 19.428 8.388 14.310 5000 4.794 19.991 19.430 8.387 14.312 5500 4.909 19.142 19.430 8.384 14.313 6000 5.317 19.153 19.432 8.383 14.315 6500 5.110 19.223 19.431 8.381 14.315 7000 4.864 19.127 19.434 8.380 14.318 7500 4.246 18.680 19.438 8.380 14.322 8000 4.508 18.937 19.438 8.377 14.322 8500 4.441 17.865 19.440 8.376 14.324 9000 4.104 19.036 19.438 8.373 14.324 9500 4.676 18.528 19.439 8.371 14.325 14.313 18.953 19.443 8.371 14.328 105004.045 18.462 19.441 8.368 14.328 110005.013 19.162 19.443 8.367 14.330 115005.131 18.435 19.446 8.366 14.333 120005.054 17.814 19.447 8.364 14.335 125004.792 17.266 19.445 8.361 14.334 130003.684 16.897 19.451 8.361 14.339 135003.885 16.450 19.451 8.359 14.340 140004.007 17.088 19.453 8.357 14.342 145003.846 17.498 19.456 8.356 14.345 snip 172500 0.619 12.210 19.702 7.999 14.791 173000 0.668 12.609 19.703 8.000 14.793 173500 0.559 12.401 19.702 7.999 14.793 174000 0.507 12.638 19.701 8.000 14.794 174500 0.518 12.512 19.697 7.998 14.792 175000 0.757 12.316 19.701 8.000 14.796 175500 0.581 12.105 19.696 7.998 14.793 176000 0.810 11.777 19.696 7.999 14.794 176500 0.763 11.521 19.694 7.998 14.794 177000 0.666 11.886 19.697 7.999 14.797 177500 0.760 11.598 19.694 7.999 14.796
[gmx-users] g_dipole ? = salt molecule in water = what is the the displacement vector pointing from the negative charge to the positive charge?
Hi molecule dipole is 48.0 sum of q_i x_i based on the following two websites, *x_i * is the displacement vectorhttp://en.wikipedia.org/wiki/Displacement_%28vector%29pointing from the negative charge to the positive charge. what about the x_i for the salt-molecule, which dissociates into one counter ion and the rest of the molecule in water? http://en.wikipedia.org/wiki/Bond_dipole_moment http://en.wikipedia.org/wiki/Electric_dipole_moment Thank you Lin On 2010-10-20 06.06, Chih-Ying Lin wrote: Hi molecule dipole is 48.0 sum of q_i x_i x_i the bond length for covalent bond. No. x_i is the atomic position. but what is x_i for salt-molecule? For salt-molecule, the ionic bonds are broken in water solvent and the counter ions are spread among the water. What is the x_i of the ionic bond in the dipole moment calculation? Is x_i equal to the distance of the two parts of the salt-molecules (the counter ion and the rest of the molecule) even though the salt molecule has dissolved in the water? I mean, is x_i equal to the length of simulation box if the counter ion and the rest of the molecule are in the two sides of the simulation box? I mean, if Gromacs takes x_i as the length of simulation box if the counter ion and the rest of the molecule are in the two sides of the simulation box? Thank you Lin Try http://en.wikipedia.org/wiki/Electric_dipole_moment , you might want to read the part about calculating dipole moments for an array of point charges, it is not difficult. 33 point charges are doable using pencil and calculator in about 10min. Do not worry about the reference point as long as your system is neutral, just set it to (0,0,0). Otherwise, take any kind of first year physics book it will contain very similar information. On 10/19/2010 05:39 AM, Chih-Ying Lin wrote: Hi According to the following website, http://en.wikipedia.org/wiki/Bond_dipole_moment \mu = \delta \, d. The bond dipole is modeled as +ä -- ä- with a distance /d/ between the partial charges http://en.wikipedia.org/wiki/Partial_charges +ä and ä-. For a complete molecule the total molecular dipole moment may be approximated as the vector sum of individual bond dipole moments. However, for a molecule of multiple atoms, There may be more than one bond connected on one atom. E | B - A - C partial charge of atom_A = -0.5 partial charge of atom_B = 0.2 partial charge of atom_C = 0.35 partial charge of atom_E = 0.4 Which partial charges should I use when I calculate bond-dipole-moment of A-B ? Which partial charges should I use when I calculate bond-dipole-moment of A-C ? Which partial charges should I use when I calculate bond-dipole-moment of A-E ? Thank you Lin On 2010-10-18 03.30, Chih-Ying Lin wrote: HI I confined one molecule in the center of box and issue the g_dipole command. The average dipole moment is still around 32. It is the molecule with 33 atoms / united atoms of most carbon groups, isn't the dipole moment around 32 too high? How can I test next and know that the dipole moment around 32 is acceptable? By calculating on paper: dipole is 48.0 sum of q_i x_i, therefore if you have large charge separation you will get a large dipole. Thank you Lin On 2010-10-16 21.36, Chih-Ying Lin wrote: Hi I issue the g_dipole command on Gromacs = And, the following information is shown. There are 10 molecules in the selection, Does the Average =32.1611 refer to the average for a single over the simulation time? Or, the Average = 32.1611 summing for all the 10 molecules over the simulation time? If the average = 32.1611 for a single molecule with 33 atoms / united atoms of most carbon groups, isn't the dipole moment too high? I think this is the average per molecule. You may need to run trjconv -pbc whole, because mdrun may break molecules in two parts, meaning that the molecule becomes as big as the box. What does will subtract their charge at their center of mass this mean? Why will subtract their charge at their center of mass ? -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20101019/4cf32833/attachment.html -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! End of gmx-users Digest, Vol 78, Issue 142 ** -- gmx-users mailing listgmx-users@gromacs.org
Re: [gmx-users] question about periodic boundary conditions
Hi, I am new to the list. I am trying to simulate lipid bilayer with atomistic model. I want to calculate surface pressure at phase boundary. I am thinking of using #surf*surfTen option with g_energy. But I am afraid, that I won't get a meaningful value because of large fluctuations. I would like to know how this option calculates surface tension? also if there exist a better way of calculating surface pressure from Gromacs data. Can anyone suggest a way or useful document to refer for this scenario. Thanks, -- - Abhijeet -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_dipole ? = salt molecule in water = should I include counter ions in my calculation?
HI 48.0 sum of q_i x_i x_i is the atomic position. For the salt molecule in water, should I include counter ions in my calculation ? Or, only the rest of the salt molecule except the counter ions? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] question about periodic boundary conditions
On 21/10/2010 10:45 AM, Abhijeet Joshi wrote: Hi, I am new to the list. I am trying to simulate lipid bilayer with atomistic model. I want to calculate surface pressure at phase boundary. I am thinking of using #surf*surfTen option with g_energy. But I am afraid, that I won't get a meaningful value because of large fluctuations. I would like to know how this option calculates surface tension? also if there exist a better way of calculating surface pressure from Gromacs data. Can anyone suggest a way or useful document to refer for this scenario. I can't help you on point, but to maximize the chance of a knowledgeable reader having their interest captured, you should write a new email with a relevant subject, rather than replying to an old one with a new topic. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Re: swiss param query
Hi all, Just as a follow-up on this one: the problem was solved by a correct ordering of the sections in the topology. The SwissParam server (www.swissparam.ch ) works correctly to generate Gromacs topologies for small organic molecules! Note that the tutorial has been updated for the case where there is only one protein chain and no ions in your PDB file (the topol.top file looks different). Enjoy, Michel On 12 oct. 10, at 14:28, gmx-users-requ...@gromacs.org wrote: From: Michel Cuendet michel.cuen...@isb-sib.ch Date: 12 octobre 2010 13:09:22 HAE (ÉUA) To: gmx-users@gromacs.org Subject: [gmx-users] Re: swiss param query Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Hi Ram, Please note that the SwissParam parameters have been tested only with the charmm force field. But this in principle shouldn't prevent you from TRYING to use these parameters (which come from the Merck Molecular Force Field in the first place) with OPLS. The error you mention should not happen, because all atomtypes needed by SwissParam should be defined in the ligand.itp file. Are you sure that you included the ligand.itp file exactly at the right place in your topol.top file? It should be done as suggested in the SwissParam tutorial: http://www.swissparam.ch/SwissParam_gromacs_tutorial.html If you are still encountering problems, please send me your ligand.itp and topol.top files offline. Best regards, Michel On 10/12/2010 11:23 AM, gmx-users-requ...@gromacs.org wrote: Part 1.2 Subject: [gmx-users] swiss param query, From: ram bio rmbio...@gmail.com Date: Tue, 12 Oct 2010 16:32:39 +0200 To: Discussion list for GROMACS users gmx-users@gromacs.org Dear Gromacs Users, I have generated the topology and parameters files for my ligand through swiss param site. Now i am trying to run a simulation of protein ligand complex in POPC bilayer using OPLS force field in Gromacs, but when I am using the grompp command in gromacs for tpr generation I am getting an error as follows: Atomtype C5A not found Please let me know your suggestions, to correct this error, I have included ligand.itp in the topology file of the protein. Thanks, ram == Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne Switzerland http://lausanne.isb-sib.ch/~mcuendet/ == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Surface pressure for lipid bilayer.
Hi, As correctly pointed out by Mark, I am restating my concern in this topic. I am trying to simulate lipid bilayer with atomistic model. I want to calculate surface pressure at phase boundary. I am thinking of using #surf*surfTen option with g_energy. But I am afraid, that I won't get a meaningful value because of large fluctuations. I would like to know how this option calculates surface tension? also if there exist a better way of calculating surface pressure from Gromacs data. Can anyone suggest a way or useful document to refer for this scenario. Thanks, -- - Abhijeet -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_dipole ? = The salt molecule = The discrepancy of dipole moment between my calculation and GROMACS
HI dipole moment = 48.0 sum of q_i x_i x_i is the atomic position. I did not include the counter ion of the salt molecule in my calculation. The salt molecule is A-N(CH3)3-Br and it has two structures, cis and trans. Here A are a string of atoms, most of them are carbons. For the cis-structure Dipole moment from GROMACS Average = 33.0312 Std. Dev. = 3.5144 Error = 0.0236 Dipole moment from my calculation = 55.8675 For the trans-structure Dipole moment from GROMACS Average = 36.8470 Std. Dev. = 3.4917 Error = 0.0238 Dipole moment from my calculation = 77.2346 Questions: 1. There is a huge discrepancy between my calculation results and GROMACS. Or, the two results are within acceptable discrepancy ??? 2. In the beginning, I suppose that the trans-structure has smaller dipole moment than cis-structure. However, it seems to be the opposite conclusion based on both GROMACS and my calculation. Is there something possible wrong ??? 3. I get the partial charges from the Journal papers and the partial charges are derived for the similar molecules as mine. Is that wrong? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
