Re: [gmx-users] Free energy calculation by MM_PBSA
Thank you. With regards, Indu On Tue, Dec 9, 2014 at 12:59 PM, Bikash Ranjan Sahoo bikash.bioinformat...@gmail.com wrote: Hi, This usually occurred when you run apbs for a large number of conformations serially. Sometimes, a big protein (800-1000 residues) also arrested the program as apbs consumes a very high memory on cluster (in my case for 500 snapshots ~400 aa long protein it consumes ~300-400GB). Try using a small number of snapshots if you are running in parallel. And if you are running one pro, lig and complex in your local computer, kindly check the CPU usage and do the needful. Core dumped usually fired with memory inadequacy. -- *BIKASH RANJAN SAHOO * *Osaka Univ. Japan* On Tue, Dec 9, 2014 at 4:16 PM, Indu Kumari kumari.ind...@gmail.com wrote: Hello everyone, I am trying to calculate free energy of protein ligand complex by using MM_PBSA method. While calculating polar solvation energy of the complex, I am getting this error. * Segmentation fault (core dumped).* *Please help!* With regards, Indu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] running solvate twice...
BSD Dear Justin, The new water molecules are scattered throughout the box. The density of the system behaves in the following manner 1. First run of solvate: 7025 waters added, density 994.192 g/l (a bit low??) 2. Run solvate on result of 1: 20 waters added, density 996.828 g/l This really shouldn't happen. How are you adding these additional waters? If it's via -ci -nmol, then I can understand there is some ability for individual molecules to find voids that might not be present when simply solvating with -cs, but there is nothing at all suspicious about the density obtained in step 1. I used -cs spc216.gro I would have thought the density should be 1000 or slightly higher, not lower. 4. Run solvate on result of 1 after adding ions, minimize, position restrained dynamics, npt dynamics: 636 waters added, density 1113.91 g/l Further driving things in the wrong direction. Moreover, I don't think it proves anything you happen to be able to flood in waters in one snapshot of a longer simulation. Voids come and go that may accommodate waters as things move around, but that doesn't mean you need to fill them. Unless your box is behaving in some bizarre way such that there are obvious, large voids, I don't see any purpose to doing all of these solvating steps. All the solvate runs I described in my previous email were only to try and trouble-shoot the issue. If you think 1 round of solvate is fine, I'm quite happy to leave off the second round. Thanks Harry - Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology Weizmann Institute of SciencePhone: 972-8-934-3625 234 Herzl St.Facsimile: 972-8-934-4159 Rehovot, 76100 Israel harry.greenbl...@weizmann.ac.ilmailto:harry.greenbl...@weizmann.ac.il -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] running solvate twice...
Hey :) Genbox takes account of VDW radii, if available. However, water is odd stuff, building cages with hydrogen bonds, like clusters with ice-like structure. My guess is that genbox considers these as cavities, based on the VDW radii. Probably having around 10% 'hits' when overlaying another water box is not even unreasonable. From the point of what genbox is written for, I don't think it's wrong. Cheers, Tsjerk On Tue, Dec 9, 2014 at 9:27 AM, Harry Mark Greenblatt harry.greenbl...@weizmann.ac.il wrote: BSD Dear Justin, The new water molecules are scattered throughout the box. The density of the system behaves in the following manner 1. First run of solvate: 7025 waters added, density 994.192 g/l (a bit low??) 2. Run solvate on result of 1: 20 waters added, density 996.828 g/l This really shouldn't happen. How are you adding these additional waters? If it's via -ci -nmol, then I can understand there is some ability for individual molecules to find voids that might not be present when simply solvating with -cs, but there is nothing at all suspicious about the density obtained in step 1. I used -cs spc216.gro I would have thought the density should be 1000 or slightly higher, not lower. 4. Run solvate on result of 1 after adding ions, minimize, position restrained dynamics, npt dynamics: 636 waters added, density 1113.91 g/l Further driving things in the wrong direction. Moreover, I don't think it proves anything you happen to be able to flood in waters in one snapshot of a longer simulation. Voids come and go that may accommodate waters as things move around, but that doesn't mean you need to fill them. Unless your box is behaving in some bizarre way such that there are obvious, large voids, I don't see any purpose to doing all of these solvating steps. All the solvate runs I described in my previous email were only to try and trouble-shoot the issue. If you think 1 round of solvate is fine, I'm quite happy to leave off the second round. Thanks Harry - Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology Weizmann Institute of SciencePhone: 972-8-934-3625 234 Herzl St.Facsimile: 972-8-934-4159 Rehovot, 76100 Israel harry.greenbl...@weizmann.ac.ilmailto:harry.greenbl...@weizmann.ac.il -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Empirical force fields: release of R.E.D. Server Dev./PyRED Nov. 2014
Dear All, I am pleased to announce the release of the R.E.D. Server Development/PyRED version November 2014 at q4md-forcefieldtools.org: http://q4md-forcefieldtools.org/REDServer-Development/ Among the new developed features this version handles the Amber non-additive force field model: - i. e. generation of polarizable force fields. The list of the new features developed in this version is available at: http://q4md-forcefieldtools.org/REDServer-Development/Bugs-NewFeatures.txt Documentation has been updated: http://q4md-forcefieldtools.org/REDServer-Development/Documentation/ New tutorials are available at: http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php The 'Re_Fit' mode, as well as the 'Complex' mode and the broken symmetry approach developed for bioinorganic complexes are described. Force field generation with lone-pairs and/or extra-points, using GAFF, OPLS and the Glycam 2004/2006 force fields, and generation of Amber polarizable force fields are also demonstrated. R.E.D. Server Development interfaces the RESP program version 2.4 or 3.1: http://q4md-forcefieldtools.org/REDServer-Development/resp/ This project is funded by the Conseil Regional de Picardie and the European Regional Development Fund. It results from a joined project between the Universite de Picardie - Jules Verne (Amiens, France) and the Sanford-Burnham Medical Research Institute (San Diego, USA) regards, Francois F.-Y. Dupradeau --- http://q4md-forcefieldtools.org/FyD/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PMF and RDF
Dear Sujith, Umbrella sampling does exactly that, but adds a biasing potential to sample high-energy regions of the reaction coordinate in separate simulations. The -px output when you do umbrella sampling with mdrun is indeed a sampling of distances along the reaction coordinate, which if you histogram it is the rdf. g_wham uses that data (or alternatively the force along the reaction coordinate instead of the distance) to build a PMF. My question to you is why do you think rdfs are significantly easier than pmfs? Kind regards, Erik On 9 Dec 2014, at 06:39, sujithkakkat . sujithk...@gmail.com wrote: Dear all, I read in *Phys. Chem. Chem. Phys., 2009, 11, 10427-10437*, that the radial distribution function is directly related to Potential of mean force through RDF=exp(-PMF/kT). My question is why would someone worry about computing PMF in a simple case like interaction between two small solute molecules in water , along the intermolecular distance, when one can get the RDF between the solutes , which I believe is easier than PMF calculation. Another article *Biophysical Chemistry 101-102 (2002), 295-307 *reports PMF between solute molecules from Monte Carlo simulations. Why not just find RDF. Regards, Sujith. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] problem during energy minimization
Hello, I am simulating a double stranded DNA in presence of choline. I am using CHARMM force field and GROMACS 4.5.6 for my simulations. I made the choline molecule as suggested by justin using CGenFF and included in my system by using -ci -nmol option of genbox. I am facing some problems in the energy minimization step which is as follows- Back Off! I just backed up emz.log to ./#emz.log.1# Reading file emz.tpr, VERSION 4.5.6 (single precision) Starting 80 threads Making 3D domain decomposition 5 x 4 x 4 Back Off! I just backed up emz.trr to ./#emz.trr.1# Back Off! I just backed up emz.edr to ./#emz.edr.1# Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up emz.gro to ./#emz.gro.1# Steepest Descents converged to machine precision in 331 steps, but did not reach the requested Fmax 1000. Potential Energy = 5.4556762e+08 Maximum force = 4.0237480e+04 on atom 919 Norm of force = 4.8998334e+02 NOTE: 7 % of the run time was spent communicating energies, you might want to use the -gcom option of mdrun My minimization.mdp file is as follows- ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; Short-range electrostatic cut-off rvdw= 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) ~ I read about 'blowing up' of the system but I dont know how to use double precission GROMACS. I cant figure out what the problem is. Is there anything wrong with the .mdp file? Is there anything wrong with my initial and solvated configurations? If not what is the way to get rid of this error? Thanks for your help and time in advance. Soumadwip Ghosh Research Fellow Indian Institute of Technology, Bombay India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PMF and RDF
On 12/9/14 1:39 AM, sujithkakkat . wrote: Dear all, I read in *Phys. Chem. Chem. Phys., 2009, 11, 10427-10437*, that the radial distribution function is directly related to Potential of mean force through RDF=exp(-PMF/kT). My question is why would someone worry about computing PMF in a simple case like interaction between two small solute molecules in water , along the intermolecular distance, when one can get the RDF between the solutes , which I believe is easier than PMF calculation. Another article *Biophysical Chemistry 101-102 (2002), 295-307 *reports PMF between solute molecules from Monte Carlo simulations. Why not just find RDF. For some systems, this may work, but only if the barriers are small enough that they can be sampled during normal MD. For instance, we recently compared PMFs from umbrella sampling and from RDF for ions in water. Given that the waters rarely displace from the ions' solvation shells (11 kcal/mol barrier in one case, for instance), there is a region with complete absence of sampling. So, in some cases it may work, and in others (likely many) it will fail for practical reasons. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] problem during energy minimization
On 12/9/14 6:51 AM, soumadwip ghosh wrote: Hello, I am simulating a double stranded DNA in presence of choline. I am using CHARMM force field and GROMACS 4.5.6 for my simulations. I made the choline molecule as suggested by justin using CGenFF and included in my system by using -ci -nmol option of genbox. I am facing some problems in the energy minimization step which is as follows- Back Off! I just backed up emz.log to ./#emz.log.1# Reading file emz.tpr, VERSION 4.5.6 (single precision) Starting 80 threads Making 3D domain decomposition 5 x 4 x 4 Back Off! I just backed up emz.trr to ./#emz.trr.1# Back Off! I just backed up emz.edr to ./#emz.edr.1# Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up emz.gro to ./#emz.gro.1# Steepest Descents converged to machine precision in 331 steps, but did not reach the requested Fmax 1000. Potential Energy = 5.4556762e+08 Maximum force = 4.0237480e+04 on atom 919 Norm of force = 4.8998334e+02 NOTE: 7 % of the run time was spent communicating energies, you might want to use the -gcom option of mdrun My minimization.mdp file is as follows- ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; Short-range electrostatic cut-off rvdw= 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) ~ I read about 'blowing up' of the system but I dont know how to use double precission GROMACS. I cant figure out what the problem is. Is there anything wrong with the .mdp file? Is there anything wrong with my initial and solvated configurations? If not what is the way to get rid of this error? Yes, your nonbonded parameters are wrong, though it's probably not the cause of the issue. See http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM To solve the issue, you have to do things scientifically - split the system into simpler components to narrow down the cause. What is the atom on which Fmax is acting? What is around it? Are the bonded and nonbonded parameters correctly assigned for that atom and anything to which it is connected? Test the ligand topology - does it minimize alone in vacuo, and in water? Does the DNA minimize on its own? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Gromacs 5.0.3 released
Hi Gromacs users, The official release of Gromacs 5.0.3 is available! It contains several bug fixes. Please see the link to the release notes below for more details. There are also some minor performance enhancements, warnings and documentation fixes. We encourage all users to upgrade their installations from earlier 5.0 releases. You can find the code, manual, release notes, installation instructions and test suite at the links below. ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.3.tar.gz ftp://ftp.gromacs.org/pub/manual/manual-5.0.3.pdf http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x#Release_notes_for_5.0.3 http://www.gromacs.org/Documentation/Installation_Instructions_for_5.0 http://gerrit.gromacs.org/download/regressiontests-5.0.3.tar.gz Happy simulating! Mark Abraham Gromacs development manager -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PMF and RDF
On 9 Dec 2014, at 11:00, Erik Marklund erik.markl...@chem.ox.ac.uk wrote: Dear Sujith, Umbrella sampling does exactly that, but adds a biasing potential to sample high-energy regions of the reaction coordinate in separate simulations. The -px output when you do umbrella sampling with mdrun is indeed a sampling of distances along the reaction coordinate, which if you histogram it is the rdf. g_wham uses that data (or alternatively the force along the reaction coordinate instead of the distance) to build a PMF. My question to you is why do you think rdfs are significantly easier than pmts? To clarify what I meant, in light of what Justin wrote earlier, is that the pmf and ref can *in principle* be calculated from exactly the same data. The *conventional* way to get the pmf involves biasing the simulations to sample poorly populated regions, whereas the rdf is commonly inferred from simulations without such bias. In principle the rdf can also be obtained from biased simulations if that bias is corrected for during analysis, and similarly a pmf can be obtained without bias. As Justin said, there are many situations where the sampling is insufficient for some distances however. Erik Kind regards, Erik On 9 Dec 2014, at 06:39, sujithkakkat . sujithk...@gmail.com wrote: Dear all, I read in *Phys. Chem. Chem. Phys., 2009, 11, 10427-10437*, that the radial distribution function is directly related to Potential of mean force through RDF=exp(-PMF/kT). My question is why would someone worry about computing PMF in a simple case like interaction between two small solute molecules in water , along the intermolecular distance, when one can get the RDF between the solutes , which I believe is easier than PMF calculation. Another article *Biophysical Chemistry 101-102 (2002), 295-307 *reports PMF between solute molecules from Monte Carlo simulations. Why not just find RDF. Regards, Sujith. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Question on installation
May be just let gromacs build its own fftw3 library, by using -DGMX_BUILD_OWN_FFTW=ON in the cmake command, is a better idea? On Mon, Dec 8, 2014 at 2:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/8/14 12:38 PM, Igor Shchechkin wrote: Dear Gromacs users, I have obtained the error Cannot find fftw3f library installing 4.5.3 version of Gromacs. fftw 3.3.4 version has been preliminary installed, names of include and lib directories present in CPPFLAGS and LDFLAGS configuring Gromacs, both FFTW and Gromacs are configured in single precision. Mailing list is sought and the information found is irrelevant to my case. Could you, please, help me? You need to provide the actual command(s) you issued. If FFTW is installed, whatever you specified as a path during Gromacs installation was probably just wrong. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Dihedral angle calculation in Gromacs
what do you mean by tensor? On Fri, Nov 28, 2014 at 4:22 AM, Ankit Agrawal aka...@gmail.com wrote: Hi I have pdb file which has crystal structure of Cadherin-23 (2WHV) with 2 domains EC1 EC2. So I want to calculate angle between two domains (tensor) along with the principal axes. regards Ankit -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Your solvent group size (*) is not a multiple of *
Dear Gromacs Users, I'm new in gromacs and I have been trying to add ions to the simulation box using following command in gromacs 5: gmx genion -s ions.tpr -o conf-ion.pdb -p topol.top -neutral -conc 0.15 then I selected these groups(Protein, MG, Ligand, respectively): 1 | 13 | 14 This error was appeared: Program gmx, VERSION 5.0 Source code file: /home/QMMM/ProgramFiles/gromacs-5.0/src/gromacs/gmxana/gmx_genion.c, line: 503 Fatal error: Your solvent group size (2701) is not a multiple of 9 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I found this URL http://comments.gmane.org/gmane.science.biology.gromacs.user/64577; in related to my question but i don't understand answer to resolve my error? Indeed, I 've already successfully simulated another protein with same gromacs and commands. Thank You in Advance -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Your solvent group size (*) is not a multiple of *
On 12/9/14 9:25 AM, Hassan Aaryapour wrote: Dear Gromacs Users, I'm new in gromacs and I have been trying to add ions to the simulation box using following command in gromacs 5: gmx genion -s ions.tpr -o conf-ion.pdb -p topol.top -neutral -conc 0.15 then I selected these groups(Protein, MG, Ligand, respectively): 1 | 13 | 14 This error was appeared: Program gmx, VERSION 5.0 Source code file: /home/QMMM/ProgramFiles/gromacs-5.0/src/gromacs/gmxana/gmx_genion.c, line: 503 Fatal error: Your solvent group size (2701) is not a multiple of 9 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I found this URL http://comments.gmane.org/gmane.science.biology.gromacs.user/64577; in related to my question but i don't understand answer to resolve my error? Indeed, I 've already successfully simulated another protein with same gromacs and commands. You shouldn't be replacing a merged group of protein, Mg, and ligand with ions. You need to choose some sort of solvent (water) with ions. This requires no custom group to do. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Possible bugs: Problems about the 12-6 WALL used with NPT systems.
Dear Users, I have did lots of tests on a simple systems which only contain a water box and two 12-6 walls at z=0 and z=box. The simulations are performed in NPT with only semi-isotropic pressure coupling applied in z-direction. And of course the 2-d Ewald will be used in this simulation with ewald_geometry=3dc and PBC = XY. However, in this simple system, the box length in z dimension keep increasing and results in a increased vacuum in the simulation box. Then by changing the wall-type to be 10-4, the pressure coupling works well with the vacuum disappearing (water density is also perfect). For your information, I have given the parameters I used in the simulation below. For 10-4 and 12-6 wall, in mdp file we only need to revise two parameters (wall_type and wall_density), as given below. I did this test in Gormacs 4.0/4.5/5.0. Actually this is also true for wall table potentials used with NPT systems. # pbc = xy coulombtype = PME rcoulomb = 1.3; 1.0 vdwtype = switch rvdw = 1.2; 0.9 rvdw_switch = 1.0; 0.8 ewald_geometry = 3dc tcoupl = nose-hoover tc_grps = System tau_t = 0.1 ref_t = 310 ;pcoupl = no pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 15.0 15.0 ref_p = 0 1.0 compressibility = 0 4.5e-5 nwall = 2 wall_type = 12-6; for 12-6 wall, and 10-4 used for 10-4 wall wall_r_linpot = 0.0 wall_atomtype = opls oplswall_density = 114 114, only for 10-4 wall, for 12-6, no this term. wall_ewald_zfac = 3 ### If you have any suggestion about it, please let me know. Thanks a lot. Best Jerry -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Protein distance with respect to box walls
Try to use the VMD to directly measure the distance between the protein and box boundary. On Tuesday, December 9, 2014 8:16 AM, Smith, Micholas D. smit...@ornl.gov wrote: Hi James, The utility g_mindist lets you measure the minimum distance between a selection and its periodic image, if what you are trying to do is just confirm that your simulation box is large enough to prevent periodic image effects, this is one way to check. Kind Regards, Micholas === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of a...@imtech.res.in a...@imtech.res.in Sent: Monday, December 08, 2014 11:39 PM To: Gmx users Subject: Re: [gmx-users] Protein distance with respect to box walls Dear James, I think if you load your system in VMD you can measure the dimensions of protein with something like set sel [atomselect top protein] measure minmax $sel Regards. Amin. On 2014-12-09 08:55, James Lord wrote: Dear Users, I have a protein in a box and was wondering to know how to figure out the protein distance to the box walls? I can see the box dimensions at the end of .gro file but how to know what is (x,y,z) of protein in the box?? any comments? Cheers James -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] gromacs on GPU
Dear users and developers, I have installed gromacs 4.6.7 with GPU enabled (with CUDA 6.5). I want to do some testing calculations to see the performance on GPU. Could someone provide some input files that are good for testing GPU performance? Has anyone successfully installed gromacs 5.0 with GPU enabled? I got errors from the self-included boost tool (see below). But these errors disappear if I installed CPU-only gromacs 5.0. === Error message: --- .. ... gromacs-5.0/src/external/boost/boost/config/suffix.hpp(496): error: identifier __int128 is undefined ... gromacs-5.0/src/external/boost/boost/config/suffix.hpp(497): error: expected a ; .. == Thank you! Best, Shaohao -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gromacs on GPU
Hi Shaohao, This is caused by a boost bug that affects the nvcc CUDA compiler, for details see: https://svn.boost.org/trac/boost/ticket/8048 Either of the following should work: i) use this workaround: appedn to src/external/boost/boost/config/compiler/nvcc.hpp #if defined(BOOST_HAS_INT128) defined(__CUDACC__) #undef BOOST_HAS_INT128 #endif ii) install boost from a fairly fresh git version (the bug was fixed on Oct 10 for 1.57: https://github.com/boostorg/config/commit/441311c950a40b9bea824016e9e43d7af5e3d4b0) Cheers, -- Szilárd On Tue, Dec 9, 2014 at 5:50 PM, Shaohao Chen shaohaoc...@cct.lsu.edu wrote: Dear users and developers, I have installed gromacs 4.6.7 with GPU enabled (with CUDA 6.5). I want to do some testing calculations to see the performance on GPU. Could someone provide some input files that are good for testing GPU performance? Has anyone successfully installed gromacs 5.0 with GPU enabled? I got errors from the self-included boost tool (see below). But these errors disappear if I installed CPU-only gromacs 5.0. === Error message: --- .. ... gromacs-5.0/src/external/boost/boost/config/suffix.hpp(496): error: identifier __int128 is undefined ... gromacs-5.0/src/external/boost/boost/config/suffix.hpp(497): error: expected a ; .. == Thank you! Best, Shaohao -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Protein distance with respect to box walls
Hi, The location of the box boundary is irrelevant in virtually all cases, unlike the distance to the periodic image. Why do you need to know the distance to the box? Note that regardless of box angles the simulation cell will be represented as a cuboid within mdrun anyway. Erik On 9 Dec 2014, at 16:55, xu zhijun simulatio...@yahoo.com wrote: Try to use the VMD to directly measure the distance between the protein and box boundary. On Tuesday, December 9, 2014 8:16 AM, Smith, Micholas D. smit...@ornl.gov wrote: Hi James, The utility g_mindist lets you measure the minimum distance between a selection and its periodic image, if what you are trying to do is just confirm that your simulation box is large enough to prevent periodic image effects, this is one way to check. Kind Regards, Micholas === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of a...@imtech.res.in a...@imtech.res.in Sent: Monday, December 08, 2014 11:39 PM To: Gmx users Subject: Re: [gmx-users] Protein distance with respect to box walls Dear James, I think if you load your system in VMD you can measure the dimensions of protein with something like set sel [atomselect top protein] measure minmax $sel Regards. Amin. On 2014-12-09 08:55, James Lord wrote: Dear Users, I have a protein in a box and was wondering to know how to figure out the protein distance to the box walls? I can see the box dimensions at the end of .gro file but how to know what is (x,y,z) of protein in the box?? any comments? Cheers James -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PMF and RDF
Hi Erik and Justin, Thanks for the response. Erik, I was thinking that in the case of hydrophobic solutes, there is a higher chance of proper sampling of all points along the inter solute distance. I believe the water shell around the hydrophibic solvent can break easier than the that in the case of ions. In that case I hope standard simulations can give better solute-solute RDFs and PMF may be avoided. The article which I refered to studies hydrophobic solutes and they have done PMF calculations. Regards, Sujith. On Tue, Dec 9, 2014 at 7:41 PM, Erik Marklund erik.markl...@chem.ox.ac.uk wrote: On 9 Dec 2014, at 11:00, Erik Marklund erik.markl...@chem.ox.ac.uk wrote: Dear Sujith, Umbrella sampling does exactly that, but adds a biasing potential to sample high-energy regions of the reaction coordinate in separate simulations. The -px output when you do umbrella sampling with mdrun is indeed a sampling of distances along the reaction coordinate, which if you histogram it is the rdf. g_wham uses that data (or alternatively the force along the reaction coordinate instead of the distance) to build a PMF. My question to you is why do you think rdfs are significantly easier than pmts? To clarify what I meant, in light of what Justin wrote earlier, is that the pmf and ref can *in principle* be calculated from exactly the same data. The *conventional* way to get the pmf involves biasing the simulations to sample poorly populated regions, whereas the rdf is commonly inferred from simulations without such bias. In principle the rdf can also be obtained from biased simulations if that bias is corrected for during analysis, and similarly a pmf can be obtained without bias. As Justin said, there are many situations where the sampling is insufficient for some distances however. Erik Kind regards, Erik On 9 Dec 2014, at 06:39, sujithkakkat . sujithk...@gmail.com wrote: Dear all, I read in *Phys. Chem. Chem. Phys., 2009, 11, 10427-10437*, that the radial distribution function is directly related to Potential of mean force through RDF=exp(-PMF/kT). My question is why would someone worry about computing PMF in a simple case like interaction between two small solute molecules in water , along the intermolecular distance, when one can get the RDF between the solutes , which I believe is easier than PMF calculation. Another article *Biophysical Chemistry 101-102 (2002), 295-307 *reports PMF between solute molecules from Monte Carlo simulations. Why not just find RDF. Regards, Sujith. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Regarding Gromacs 5.0.3 parallel computation
Dear All, I have installed the Gromacs 5.0.3 in cluster and would like to thank Dr. Mark for his valuable suggestions and guidance. I am facing some problems in the computation speed in 5.0.3. A comparable study of the same system in gromacs 4.5.5 and 5.0.3 in the same cluster using equal number of nodes rendered an extremely slow simulation for the latter one. The commands I used for installation are pasted below. cmake .. -DCMAKE_INSTALL_PREFIX=/user1/GROMACS-5.0.3 -DGMX_MPI=ON -DGMX_THREAD_MPI=ON -DGMX_PREFER_STATIC_LIBS=ON -DGMX_BUILD_OWN_FFTW=ON -DGMX_X11=OFF -DGMX_CPU_ACCELERATION=SSE4.1 I tried to do a small simulation in Gromacs 4.5.5 using 30 cores for 200 ps. The computation time was 4.56 minutes . The command used was dplace -c 0-29 mdrun -v -s md.tpr -c md.gro -nt 30 . Next I ran the same system using Gromacs 5.0.3. The command used was dplace -c 0-29 mpirun -np 30 mdrun_mpi -v -s md.tpr -c md.gro. The simulation was extremely slow and took 37 minutes to complete only 200 ps MD. Even the energy minimization for a small protein is taking long time in 5.0.3 which can be converged in 4.5.5 in few seconds. Kindly suggest me where is the problem. Is there any problem in my installation procedure (in cmake commands). Thanking You In anticipation of your reply. Bikash, Osaka, Japan P.S. The dplace 0-29 is for serial assignment of CPUs in my cluster. Kindly ignore it if you are using qsub. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] ProDrg
How about ACPYPE for AMBER force field? On Tue, Dec 9, 2014 at 12:56 AM, Justin Lemkul jalem...@vt.edu wrote: On 12/8/14 2:12 PM, xy21hb wrote: Dear all, Since Justin mentioned in previous mails that PRODRG is almost unreliable, is there any reliable source for patching a new small molecule for gromacs, in general? When it comes to force fields, you can't speak in generalities. Any new species must be parametrized in accordance with the methods of the parent force field, for balance and consistency. The ATB server is significantly better than PRODRG for Gromos-compatible compounds. There are other servers for other force fields (ParamChem for CHARMM/CGenFF, etc) but no black-box method should be trusted without scrutinizing and testing extensively. The bottom line is that parametrization of new species is hard, and it often requires significant effort in finding suitable target data, refining parameters to match, then validating that those parameters are actually useful in subsequent simulations. This is common across all simulation codes and all force fields. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Nabajyoti Goswami Research Associate Bioinformatics Infrastructure Facility Department of Animal Biotechnology College of Veterinary Science Khanapara,Guwahati 781022 Assam, India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
