[gmx-users] pressure simulation along the z-axis
Hi all, I have a box containing several strands of some biopolymers and I want to do a simulation of this box fixing the X and Y direction, while applying pressure only along the Z axis. Can anybody please tell me how to achieve this? Best, Felipe -- 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] pressure simulation along the z-axis
On 2/2/15 4:41 PM, felipe zapata wrote: Hi all, I have a box containing several strands of some biopolymers and I want to do a simulation of this box fixing the X and Y direction, while applying pressure only along the Z axis. Can anybody please tell me how to achieve this? Use semiisotropic pressure coupling and set the x-y compressibility to zero. -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] q-bio Summer School 2015
Dear all, there will be a GROMACS tutorial as part of the q-bio Summer School 2015 at the University of New Mexico in Albuquerque, NM (details below). Cheers, Christoph --- Original Announcement: Dear Faculty, Students and Postdocs, We are pleased to announce that applications are now being accepted for the Ninth Annual q-bio Summer School. The application requires a CV and a 1-page statement of interest in the summer school (combined into a singe .pdf). Scholarships are available. _Applications will be due on*Monday, February 16 at 11:59pm (MST)*_. Submitted applications may be revised until that time. To apply now, please visit our website: http://q-bio.org/wiki/The_Ninth_q-bio_Summer_School The q-bio Summer School will cover nine different general topic areas and be held at *three different campuses*. The specific dates and campus locations are: 1. July 6-21, 2015 at the Colorado State University in Fort Collins, CO 2. July 13-28, 2015 at the University of New Mexico in Albuquerque, NM 3. July 13-28, 2015 at the University of California in San Diego, CA. *School Overview:* The q-bio Summer School is an annual event intended to advance predictive modeling of cellular regulatory systems by exposing participants to a survey of work in quantitative biology and by providing in-depth instruction in selected techniques, with an emphasis on techniques useful for modeling cellular regulatory networks. Certain data analysis techniques and experimental methods will also be covered. Lectures will be offered at *three campuses.* At the *San Diego campus*, the focus will be on synthetic biology. At the *Albuquerque and Fort Collins campuses*, the focus will be on different aspects of systems biology. Students will each work on a mentored project in one of the following areas: stochastic gene regulation, cell signaling, biomolecular simulations, viral dynamics, cancer dynamics, fluorescence imaging and imaging data analysis, and experimental/computational/theoretical methods in synthetic biology. Participants will attend daily core lectures, project-specific lectures, journal clubs, and computer and experimental labs. The summer school is designed for graduate students, postdocs, or anyone with a quantitative background who is new to modeling cellular regulatory systems/networks. After completion of the school, all students are strongly encouraged to attend either the Ninth q-bio Conference in Blacksburg, VA (August 5-8, 2015) or the Fourth Winter q-bio Meeting (TBA). *The main topics of the 2015 summer school are:* * Biomolecular Simulations (Albuquerque, NM) * Cell Signaling (Albuquerque, NM) * Membrane Biology (Albuquerque, NM) * Viral Dynamics (Albuquerque, NM) * Cancer Dynamics (Fort Collins, CO) * Complex Biological Dynamics (Fort Collins, CO) * Stochastic Gene Regulation (Fort Collins, CO) * Computational Synthetic Biology (San Diego, CA) * Experimental Synthetic Biology (San Diego, CA) Please see the school wiki (http://q-bio.org/wiki/The_Ninth_q-bio_Summer_School) for more information about each specific topic. At the School, students will attend 20-25 hours of core lectures, 20-25 hours of course-specific lectures, 10-15 hours of computational and experimental labs, and 10-15 hours of student presentations. There will also be 20-30 hours of mentored project work, which may include some simple experiments, theoretical developments and/or real data analyses. Questions? Please see our FAQs page on wiki site first, or contact our program manager, Shannan Yeager, at the address below. *Organizers:* * S. Gnanakaran, New Mexico Consortium, Los Alamos * Jeff M. Hasty, University of California, San Diego * William S. Hlavacek, New Mexico Consortium, Los Alamos * Marek Kimmel, Rice University, Houston * Brian Munsky, Colorado State University, Fort Collins * Ashok Prasad, Colorado State University, Fort Collins * Douglas Shepherd, University of Colorado, Denver * Patrick Shipman, Colorado State University, Fort Collins * Mara P. Steinkamp, University of New Mexico, Albuquerque * Lev S. Tsimring, University of California, San Diego *For inquiries about the scientific content at the summer school, please contact:* * Brian Munsky (Fort Collins Campus): mun...@engr.colostate.edu * Bill Hlavacek (Albuquerque Campus): wshlava...@gmail.com * Lev Tsimring (San Diego Campus): ltsimr...@ucsd.edu *Point of Contact*: Shannan Yeager, q-bio Program Manager, syea...@newmexicoconsortium.org For more information, please visit the school wiki at:http://q-bio.org/wiki/The_Ninth_q-bio_Summer_School Please visit and join the q-bio group on LinkedIn: http://www.linkedin.com/groups/qbio-5075101 *Online Application website: https://www.openconf.org/qbioss2015/openconf.php -- Christoph Junghans Web: http://www.compphys.de -- Gromacs Users mailing list * Please search the archive at
Re: [gmx-users] Umbrella Samling Alteration
On 2/1/15 11:22 PM, Alexander Law wrote: Dear Gromacs Users I am currently running the series of simulations using the following command: mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg I wish to lessen the amount of time for each of these simulations from 10 ns to 6 ns. These simulations are already up to around 5 ns, is it possible to change the time to 6 ns without altering the md_umbrella.mdp file and starting agin? Also, will this reduction have any major impacts on the quality/efficacy of the data? Use mdrun command-line option -nsteps to override the number of steps specified in the .tpr file, but you can't do this if the runs are in progress. -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] topology and parameter set up
On 2/2/15 8:20 AM, Jennifer Vo wrote: Dear Justin, Many thanks for your help. My em.mdp is integrator = steep emtol = 100.0 emstep = 0.01 nsteps = 10 coulombtype = PME pbc = xyz My nvt.mdp is title = Protein-ligand complex NVT equilibration define = -DPOSRES -DPOSRES_LIG ; position restrain the protein and ligand ; Run parameters integrator = md; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1.0 ps nstvout = 500 ; save velocities every 1.0 ps nstenergy = 500 ; save energies every 1.0 ps nstlog = 500 ; update log file every 1.0 ps energygrps = Protein NPD ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = hbonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 10; 20 fs, largely irrelevant with Verlet rcoulomb= 1.4 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein_NPD Water_and_ions; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 300 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed It generated no error in the log file. This is em.log Steepest Descents converged to Fmax 100 in 10536 steps Potential Energy = -2.1753502e+06 Maximum force = 8.4056786e+01 on atom 12 Norm of force = 4.0102091e+00 For the NPT.mdp, since I have got error from the previous run, so I tried commenting out the neighborsearching part to take the default number and there is still error as the previous email. This doesn't make sense to me. Please copy and paste error messages rather than trying to remember or reinterpret them. Changing the nonbonded setup midway through a run (or between stages) is fundamentally unsound. Verify that your settings are right; IIRC a 1.4-nm cutoff is wrong for AMBER force fields. -Justin Regarding the coordinates, I merged 2 coordinate files into 1 file as your tutorial about Protein-Ligand Simulation ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html) and run a genconf to renumber the system, editconf to create the cubic box and genbox to solvate the system. Then I add 24 NA since the charge of the whole system is -24. I don't know which step is a possible cause to the error. Regards, Jennifer On Mon, Feb 2, 2015 at 1:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/2/15 6:37 AM, Jennifer Vo wrote: Dear Experts, I am facing the problem of simulation of protein - ligand complex using amber99sb force field. Since I created a topol.top for the system ; Include forcefield parameters #include amber99sb.ff/forcefield.itp [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb CA CA 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 H4 H4 0.0 0.0 A 2.51055e-01 6.27600e-02 ; 1.41 0.0150 HA HA 0.0 0.0 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150 CC 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 OO 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 NN 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 HH 0.0 0.0 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157 N* N* 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CT CT 0.0 0.0 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 H2 H2 0.0 0.0 A 2.29317e-01 6.56888e-02 ; 1.29 0.0157 H1 H1 0.0 0.0 A 2.47135e-01 6.56888e-02 ;
[gmx-users] ngmx tools
Dear Justin,I'm using the GROMACS 5.0 , it seems that there isn't ngmx tool in this version, would you please help me? Which command(s) must be used for visualization?Thanks,Mrs.Mahdavi -- 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] Covalent bond/crosslink formation with calcium
On 2/2/15 7:08 AM, Turgay Cakmak wrote: Dear Gromacs users, We are simulating a large nanofiber assembly composed of repeating units of peptides, and we have been trying to see how the addition of calcium would affect its behavior. We have already tried adding calcium ions in a random distribution, which we successfully did. But we also would like to insert calcium ions directly within the fiber structure, near areas with negative charges that the calcium cation can potentially bind. Is such a configuration possible (or sensible) to simulate in Gromacs? Anything is possible. You'll have to justify if it's sensible :) Likewise, we would like to specify a number of covalent bonds between some of these side chains and the calcium ions, representing a well-crosslinked system. Is this possible, and if so, do you know of a suitable set of calcium forcefield parameters for the task? I have never heard of such bonded parameters. People usually just modify nonbonded parameters to get proper coordination geometry. Divalent metal ions are quite tricky, and most force field parameters are pretty bad approximations of the true nature of the actual interactions. You'll almost certainly have to derive suitable parameters, which will involve reparametrization of charges, because charge-transfer effects would be significant in such a complex. Simply slapping a covalent bond between some peptide group and an ion with +2 charge is likely too crude to be realistic. -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] combine two solvent box to one large box.
hello all I have made two solvent boxes with DIFFERENT protein in each box, the box have the same X-Y-Z length. I want to combine two boxes to one large box at one dimension like X or Y Witch command could do that?? best regard Cao, PhD Institute of Physics Nankai University Tianjin, China -- 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] Force field For Protein-Ligand Complex
On 2/2/15 3:36 AM, neha bharti wrote: Hello All I have to perform molecular dynamics simulation of protein-ligand complex in water. Initially I tried using gromos force field but there is some problem in its ligand itp file which is generated by PRODRG server. I also tried it with the help of ATB but again its giving error. Can I use CHARMM 27 or Charmm 36 force field for the same. Is there any reference paper?? You can do any protein-ligand complex simulation with any force field; it's all just a matter of how easy it is to generate ligand parameters. For CHARMM, use the ParamChem server. There are analogous servers and programs for AMBER, as well. -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] Significant differences in Ewald Vs PME for clay sheet
Hi Mark, We have done repeat calculations with version 5.0.4. To briefly give you the main results-- 1. Both versions, 4.5.1 and 5.0.4, with either Ewald and PME give the same values for potential energy and interparticle forces. 2. Ewald (gromacs version 5.0.4), PME (5.0.4) and PME (4.5.1) give the same result for the virials also. Only Ewald (4.5.1) is different. However. only Ewald (4.5.1) matches the sheet size and Young's modulus as obtained by force field developers. 3. Use of 3d or 3dc does not change the above determination. Details: Fourierspacing =0.08; rc=1.2 nm; ewald_rtol=1e-5; geometry=3d in all cases. Increasing accuracy of PME does not affect results. Case 1. Ewald / 4.5.1 Case 2: PME / 4.5.1 case 3: Ewald / 5.0.4 case 4; PME / 5.0.4 Ew/4.5.1 PME/4.5.1 Ew/5.0.4 PME/5.0.4 Total PE: -404119 -404118 -404112 -404113 Note 1: Individual contributions to the total PE in all 4 cases are similarly matching. Note 2: Force versus atom plots as obtained from .trr file is again matching in the four cases. However, the various virial contributions differ significantly between case 1 and rest: Ew/4.5.1 PME/4.5.1 Ew/5.0.4 PME/5.0.4 Vir-xx: 7444.71 -43309.3-43317.7 -43315.8 Vir-yy: -6327.84 -56862.3 -56869.5 -56869.5 Above numbers clearly indicate a large compressive pressure in cases 2-4 (PME), that is commensurate with observed increase in sheet size along x- and y- directions in (semi-isotropic) NPT ensemble at zero pressure. So in absence of any other data we can say something funky was happening in virial calculation with Ewald/4.5.1 which was rectified in version 5.0.4. However, Ewald/4.5.1 is the only case that matches with simulations of Heinz et al. done using the molecular studio package. Any suggestions? Thanks, G On Sun, Jan 25, 2015 at 6:25 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Sat, Jan 24, 2015 at 6:48 AM, Gaurav Goel gauravgoel...@gmail.com wrote: Hi mark, We have used version 4.5.1. Ewald_geometry = 3d gives exactly same results as 3dc. E.g., viral_xx is -43303.7 in former and -43303.8 in latter. OK, thanks. In practice, probably only Berk has any clue what this code does and how, and if there's a problem then we'd need to know whether it still exists in the latest versions (e.g. 5.0.4). Can you try that on your inputs, please? Mark Regards, G On 23-Jan-2015 10:28 pm, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, What do you see with ewald_geometry=3d? In what GROMACS version? Mark On Fri, Jan 23, 2015 at 5:47 PM, Gaurav Goel gauravgoel...@gmail.com wrote: A (brief) background: We have prepared a periodic Na-MMT clay sheet using force-field parameters as developed by Heinz and co-workers. The box (and clay sheet) are 2.6-2.7 nm in x- and y- directions. Sheet thickness along z is 0.7nm and we add a vacuum layer to get a box_z=4nm. On using Ewald summation for electrostatic interactions, we get an exact correspondence with results of Heinz et al. The equilibrium box-size in 2.6nm in x and y, as reported by Heinz using Ewald summations. Further the Young's modulus values are in close agreement with other simulation studies as well as experimental data. However when we use PME electrostatics, we see the equilibrium box size increases to 2.7nm. Also, the Young's modulus values are doubled compared to Ewald summations. This prompted us to dig more into the energy and force values. *** *** As test case, we took a single snapshot of Ewald summation equilibrated clay sheet configuration (box dimensions: 2.6 x 2.6 x 4 nm) and using 'mdrun -rerun' determined the potential energy, forces and virial components. Details are below: Case 1. Ewald (fourierspacing=0.12 ~ 40 wave vectors; ewald_rtol: 1e-5; rc=1.2nm) Case 2: PME (fourierspacin=0.08; ewald_rtol: 1e-7; pme_order 8; ewald_3dc; rc=1.2nm) We have tried a few other combinations, such as standard Ewald-PME instead of ewald_3dc, but all the numbers are same as case 2. Case 1(Ewald)case 2 (PME) Total PE: -404119 -404118 Note 1: Individual contributions to the total PE in both cases are similarly matching. Note 2: Force versus atom plots as obtained from .trr file is again exactly matching in the two cases. However, the various Virial contributions differ significantly: Vir-xx: 7444.71 -43303.8 Vir-yy: -6327.84 -56858.7 Above numbers clearly indicate a large compressive pressure in case 2 (PME), that is commensurate with observed increase in sheet size along x- and y- directions
Re: [gmx-users] topology and parameter set up
On 2/2/15 6:37 AM, Jennifer Vo wrote: Dear Experts, I am facing the problem of simulation of protein - ligand complex using amber99sb force field. Since I created a topol.top for the system ; Include forcefield parameters #include amber99sb.ff/forcefield.itp [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb CA CA 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 H4 H4 0.0 0.0 A 2.51055e-01 6.27600e-02 ; 1.41 0.0150 HA HA 0.0 0.0 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150 CC 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 OO 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 NN 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 HH 0.0 0.0 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157 N* N* 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CT CT 0.0 0.0 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 H2 H2 0.0 0.0 A 2.29317e-01 6.56888e-02 ; 1.29 0.0157 H1 H1 0.0 0.0 A 2.47135e-01 6.56888e-02 ; 1.39 0.0157 OH OH 0.0 0.0 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 HO HO 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. OS OS 0.0 0.0 A 3.1e-01 7.11280e-01 ; 1.68 0.1700 PP 0.0 0.0 A 3.74177e-01 8.36800e-01 ; 2.10 0.2000 O2 O2 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 CK CK 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 H5 H5 0.0 0.0 A 2.42146e-01 6.27600e-02 ; 1.36 0.0150 NB NB 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CB CB 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 N2 N2 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 NC NC 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CQ CQ 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 ; Include chain topologies #include A.itp ; Include Position restraint file #ifdef POSRES #include posre_A.itp #endif ; Include chain topologies #include B.itp ; Include Position restraint file #ifdef POSRES #include posre_B.itp #endif ; Include custom ligand topologies #include npd.itp ; Ligand position restraints #ifdef POSRES_LIG #include posre_npd.itp #endif ; Include water topology #include amber99sb.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic ion topology #include amber99sb.ff/ions.itp [ system ] ; Name system in water [ molecules ] ; Compound#mols A 1 B 1 NPD 1 SOL 42322 NA 24 The Protein and the Ligand were under energy minimization and a short MD separatedly to be sure there is no problem with the topology. But when I merge two topol.top from protein and from ligand, the error came at NPT step after successfully energy minimization and NVT This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. This is NPT.mdp title = system in water define = -DPOSRES -DPOSRES_LIG ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 50; 2 * 50 = 1000 ps, 1 ns dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 1.0 ps nstvout = 5000 ; save velocities every 1.0 ps nstenergy = 500 ; save energies every 1.0 ps nstlog = 500 ; update log file every 1.0 ps energygrps = Protein NPD ; Bond parameters continuation= yes ; Restarting after NVT constraint_algorithm= lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS
Re: [gmx-users] ngmx tools
On 2/2/15 7:18 AM, asasa qsqs wrote: Dear Justin,I'm using the GROMACS 5.0 , it seems that there isn't ngmx tool in this version, would you please help me? Which command(s) must be used for visualization?Thanks,Mrs.Mahdavi The program has been renamed gmx view in version 5.0. It's only a rudimentary viewing tool, so you are much better off with something like VMD or PyMol. -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] Compilation errors (5.0.4)
Hi, I can't think what could be going on there. What does cd build-intel-mkl-cuda find * -name gmx\* report? Are you able to compile and install gcc+CUDA? (probably slightly faster) Mark On Mon, Feb 2, 2015 at 9:57 AM, Satyabrata Das satyabrata...@gmail.com wrote: Dear All, I am trying to compile Gromacs 5.0.4 on a CPU / GPU cluster and the details are as follows: Intel compiler (12.1), Cuda 4.2, MKL Library, single, GPU =on and however unable to compile. Please see the attached file for compilation details and errors / warnings: The errors in the 'make install' stage is listed below: CMake Error at src/programs/cmake_install.cmake:42 (file): file INSTALL cannot find /export/home/satya/gromacs-5.0.4/build-intel-mkl-cuda/bin/gmx. Call Stack (most recent call first): src/cmake_install.cmake:38 (include) cmake_install.cmake:48 (include) make: *** [install] Error 1 Kindly help. With best regards, Satyabrata Das -- 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] Cluster recommendations
Hi David, On 22 Jan 2015, at 18:01, David McGiven davidmcgiv...@gmail.com wrote: Hey Karsten, Just another question. What do you think will be the performance difference between two gromacs runs with a ~100k atoms system like the one I mentioned on my first email : - 1 server with 4 AMD processors, 16 cores each (64 cores) with no GPU - 1 server with 4 AMD processors, 16 cores each (64 cores) with one GTX 980 GPU - 1 server with 2 Intel processors, 10 cores each (20 cores) like the ones you mentioned, with one or two GTX 980 GPU. I'm not interested in exact performance numbers, I just need to understand the logistics behind the CPU/GPU combinations in order to make an inteligent cluster purchase. I never benchmarked 64-core AMD nodes with GPUs. With a 80 k atoms test system using a 2 fs time step I get 24 ns/d on 64 AMD cores 6272 16 ns/d on 32 AMD cores 6380 36 ns/d on 32 AMD cores 6380 with 1x GTX 980 40 ns/d on 32 AMD cores 6380 with 2x GTX 980 27 ns/d on 20 Intel cores 2680v2 52 ns/d on 20 Intel cores 2680v2 with 1x GTX 980 62 ns/d on 20 Intel cores 2680v2 with 2x GTX 980 So unless you can get the AMD nodes very cheap, probably the 20-core Intel nodes with 1 or 2 GPUs will give you the best performance and the best performance/price. Best, Carsten Thanks again. Best, D 2015-01-16 14:46 GMT+01:00 Carsten Kutzner ckut...@gwdg.de: Hi David, On 16 Jan 2015, at 12:28, David McGiven davidmcgiv...@gmail.com wrote: Hi Carsten, Thanks for your answer. 2015-01-16 11:11 GMT+01:00 Carsten Kutzner ckut...@gwdg.de: Hi David, we are just finishing an evaluation to find out which is the optimal hardware for Gromacs setups. One of the input systems is an 80,000 atom membrane channel system and thus nearly exactly what you want to compute. The biggest benefit you will get by adding one or two consumer-class GPUs to your nodes (e.g. NVIDIA GTX 980). That will typically double your performace-to-price ratio. This is true for Intel as well as for AMD nodes, however the best ratio in our tests was observed with 10-core Intel CPUs (2670v2, 2680v2) in combination with a GTX 780Ti or 980, ideally two of those CPUs with two GPUs on a node. Was there a difference between 2670v2 (2.5 GHz) and 2680v2 (2.8 GHz) ? I'm wondering if those 0,3 GHz are significative. Or the 0,5 GHz compared to 2690v2 for the matter. There’s a significative difference in price indeed. Usually the percent improvement for Gromacs performance is not as much as the percent improvement in clock speed, so the cheaper ones will give you a higher performance-to-price ratio. I'm also wondering if the performance would be better with 16 core Intels instead of 10 core. I.e E5-2698 v3. Didn’t test those. I would like to know which other tests have you done. What about AMD ? We tested AMD 6380 with 1-2 GTX 980 GPUs, which gives about the same performance-to-price ratio as a 10 core Intel 2680v2 node with one GTX 980. The Intel node gives you a higher per-node performance, though. Unless you want to buy expensive FDR14 Infiniband, scaling across two or more of those nodes won’t be good (~0.65 parallel efficiency across 2, ~0.45 across 4 nodes using QDR infiniband), so I would advise against it and go for more sampling on single nodes. Well, that puzzles me. Why is it that you get poor performance ? Are you talking about pure CPU jobs over infiniband, or are you talking about CPU+GPU jobs over infiniband ? For a given network (e.g. QDR Infiniband), the scaling is better the lower the performance of the individual nodes. So for CPU-only nodes you will get a better scaling than for CPU+GPU nodes, which have a way higher per-node performance. How come you won’t get good performance if a great percentage of The performance is good, it is just that the parallel efficiency is not optimal for an MD system 100,000 atoms, meaning you do not get two times the performance on two nodes in parallel as compared to the aggregated performance of two individual runs. Bigger systems will have a better parallel efficiency. supercomputer centers in the world use InfiniBand ? And I'm sure lots of users here in the list use gromacs over Infiniband. I do, too :) But you get more trajectory for your money if you can wait and run on a single node. Carsten Thanks again. Best Regards, D Best, Carsten On 15 Jan 2015, at 17:35, David McGiven davidmcgiv...@gmail.com wrote: Dear Gromacs Users, We’ve got some funding to build a new cluster. It’s going to be used mainly for gromacs simulations (80% of the time). We run molecular dynamics simulations of transmembrane proteins inside a POPC lipid bilayer. In a typical system we have ~10 atoms, from which almost 1/3 correspond to water molecules. We employ usual conditions with PME for electorstatics and cutoffs for LJ interactions. I would like to hear your
Re: [gmx-users] topology and parameter set up
Dear Justin, Many thanks for your help. My em.mdp is integrator = steep emtol = 100.0 emstep = 0.01 nsteps = 10 coulombtype = PME pbc = xyz My nvt.mdp is title = Protein-ligand complex NVT equilibration define = -DPOSRES -DPOSRES_LIG ; position restrain the protein and ligand ; Run parameters integrator = md; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1.0 ps nstvout = 500 ; save velocities every 1.0 ps nstenergy = 500 ; save energies every 1.0 ps nstlog = 500 ; update log file every 1.0 ps energygrps = Protein NPD ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = hbonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 10; 20 fs, largely irrelevant with Verlet rcoulomb= 1.4 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein_NPD Water_and_ions; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 300 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed It generated no error in the log file. This is em.log Steepest Descents converged to Fmax 100 in 10536 steps Potential Energy = -2.1753502e+06 Maximum force = 8.4056786e+01 on atom 12 Norm of force = 4.0102091e+00 For the NPT.mdp, since I have got error from the previous run, so I tried commenting out the neighborsearching part to take the default number and there is still error as the previous email. Regarding the coordinates, I merged 2 coordinate files into 1 file as your tutorial about Protein-Ligand Simulation ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html) and run a genconf to renumber the system, editconf to create the cubic box and genbox to solvate the system. Then I add 24 NA since the charge of the whole system is -24. I don't know which step is a possible cause to the error. Regards, Jennifer On Mon, Feb 2, 2015 at 1:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/2/15 6:37 AM, Jennifer Vo wrote: Dear Experts, I am facing the problem of simulation of protein - ligand complex using amber99sb force field. Since I created a topol.top for the system ; Include forcefield parameters #include amber99sb.ff/forcefield.itp [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb CA CA 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 H4 H4 0.0 0.0 A 2.51055e-01 6.27600e-02 ; 1.41 0.0150 HA HA 0.0 0.0 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150 CC 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 OO 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 NN 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 HH 0.0 0.0 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157 N* N* 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CT CT 0.0 0.0 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 H2 H2 0.0 0.0 A 2.29317e-01 6.56888e-02 ; 1.29 0.0157 H1 H1 0.0 0.0 A 2.47135e-01 6.56888e-02 ; 1.39 0.0157 OH OH 0.0 0.0 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 HO HO 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. OS OS 0.0 0.0 A 3.1e-01 7.11280e-01 ; 1.68 0.1700 PP 0.0 0.0 A
[gmx-users] template.cpp compilation problem with Gromacs 5.0.4
Dear Gromacs users I would like to code my own analysis programs but I'm facing problems with template.cpp compilations with gromacs 5.0.4. Made source GMXRC. cmake goes nicely but make does not make it. Any suggestions? downgrade? Here goes cmake and make output. Thanks a lot Milton $mkdir build $cd build $ cmake .. -- The C compiler identification is GNU 4.8.2 -- The CXX compiler identification is GNU 4.8.2 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Found PkgConfig: /usr/bin/pkg-config (found version 0.26) -- checking for module 'libgromacs' -- found libgromacs, version 5.0.4 -- Looking for GromacsVersion in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; -- Looking for GromacsVersion in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; - found -- Looking for init_mtop in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; -- Looking for init_mtop in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; - found -- Looking for output_env_done in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; -- Looking for output_env_done in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; - found -- Looking for gmx_nonbonded_setup in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; -- Looking for gmx_nonbonded_setup in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; - found -- Looking for init_domdec_vsites in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; -- Looking for init_domdec_vsites in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; - found -- Boost version: 1.55.0 -- Found GROMACS: /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so GROMACS version 5.0.0 found -- Configuring done -- Generating done -- Build files have been written to: /home/milton/pesq/bta/progs/template/build $make Scanning dependencies of target template [100%] Building CXX object CMakeFiles/template.dir/template.cpp.o In file included from /usr/local/gromacs/include/gromacs/analysisdata/modules/histogram.h:49:0, from /usr/local/gromacs/include/gromacs/analysisdata.h:209, from /usr/local/gromacs/include/gromacs/trajectoryanalysis.h:279, from /home/milton/pesq/bta/progs/template/template.cpp:38: /usr/local/gromacs/include/gromacs/analysisdata/modules/../../utility/uniqueptr.h:81:12: error: ‘std::move’ has not been declared using std::move; ^ /usr/local/gromacs/include/gromacs/analysisdata/modules/../../utility/uniqueptr.h:85:13: error: ‘unique_ptr’ in namespace ‘std’ does not name a type typedef std::unique_ptrT type; ^ In file included from /usr/local/gromacs/include/gromacs/analysisdata.h:209:0, from /usr/local/gromacs/include/gromacs/trajectoryanalysis.h:279, from /home/milton/pesq/bta/progs/template/template.cpp:38: /usr/local/gromacs/include/gromacs/analysisdata/modules/histogram.h:249:9: error: ‘type’ in ‘struct gmx::gmx_unique_ptrgmx::AbstractAverageHistogram’ does not name a type typedef gmx_unique_ptrAbstractAverageHistogram::type ^ /usr/local/gromacs/include/gromacs/analysisdata/modules/histogram.h:283:9: error: ‘AverageHistogramPointer’ does not name a type AverageHistogramPointer resampleDoubleBinWidth(bool bIntegerBins) const; ^ /usr/local/gromacs/include/gromacs/analysisdata/modules/histogram.h:295:9: error: ‘AverageHistogramPointer’ does not name a type AverageHistogramPointer clone() const; ^ In file included from /usr/local/gromacs/include/gromacs/options/basicoptions.h:54:0, from /usr/local/gromacs/include/gromacs/options.h:149, from /usr/local/gromacs/include/gromacs/trajectoryanalysis.h:280, from /home/milton/pesq/bta/progs/template/template.cpp:38: /usr/local/gromacs/include/gromacs/options/abstractoption.h:73:9: error: ‘type’ in ‘struct gmx::gmx_unique_ptrgmx::AbstractOptionStorage’ does not name a type typedef gmx_unique_ptrAbstractOptionStorage::type ^ /usr/local/gromacs/include/gromacs/options/abstractoption.h:123:17: error: ‘AbstractOptionStoragePointer’ does not name a type virtual AbstractOptionStoragePointer createStorage() const = 0; ^ In file included from /usr/local/gromacs/include/gromacs/options.h:149:0, from /usr/local/gromacs/include/gromacs/trajectoryanalysis.h:280, from /home/milton/pesq/bta/progs/template/template.cpp:38: /usr/local/gromacs/include/gromacs/options/basicoptions.h:101:17: error: ‘AbstractOptionStoragePointer’ does not name a type virtual AbstractOptionStoragePointer createStorage() const;
Re: [gmx-users] DNA-protein complex - which force field to use?
Hi, On 02/02/15 10:18, Erik Marklund wrote: On 2 Feb 2015, at 01:53, Jernej Zidar jernej.zi...@gmail.commailto:jernej.zi...@gmail.com wrote: Hi everyone! I would like to study a DNA-protein complex. The protein part is composed of aminoacids covalently attached to the DNA bases. Which force field would you recommend? Based on recent experience I was thinking of using either OPLS-aa or CHARMM. OPLS-aa would be the prefered choice because it performs way better than CHARMM. At least for proteins that seems incorrect http://pubs.acs.org/doi/full/10.1021/ct2007814 The comparison here is with an old version of CHARMM. CHARMM36 is supposed to be way better now. In any case, If you are working with DNA the best choice seems to still be Amber-ff99sb with the bsc0 correction. I would actually use something like Amber-ff99sb*-ildn-bsc0. All those modifications are already available to be read in gromacs around. Best Felipe Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow, Fulford JRF Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ Any recommendations or experiences? Thanks in advance! Jernej -- 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.orgmailto: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] topology and parameter set up
Dear Experts, I am facing the problem of simulation of protein - ligand complex using amber99sb force field. Since I created a topol.top for the system ; Include forcefield parameters #include amber99sb.ff/forcefield.itp [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb CA CA 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 H4 H4 0.0 0.0 A 2.51055e-01 6.27600e-02 ; 1.41 0.0150 HA HA 0.0 0.0 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150 CC 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 OO 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 NN 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 HH 0.0 0.0 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157 N* N* 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CT CT 0.0 0.0 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 H2 H2 0.0 0.0 A 2.29317e-01 6.56888e-02 ; 1.29 0.0157 H1 H1 0.0 0.0 A 2.47135e-01 6.56888e-02 ; 1.39 0.0157 OH OH 0.0 0.0 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 HO HO 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. OS OS 0.0 0.0 A 3.1e-01 7.11280e-01 ; 1.68 0.1700 PP 0.0 0.0 A 3.74177e-01 8.36800e-01 ; 2.10 0.2000 O2 O2 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 CK CK 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 H5 H5 0.0 0.0 A 2.42146e-01 6.27600e-02 ; 1.36 0.0150 NB NB 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CB CB 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 N2 N2 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 NC NC 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CQ CQ 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 ; Include chain topologies #include A.itp ; Include Position restraint file #ifdef POSRES #include posre_A.itp #endif ; Include chain topologies #include B.itp ; Include Position restraint file #ifdef POSRES #include posre_B.itp #endif ; Include custom ligand topologies #include npd.itp ; Ligand position restraints #ifdef POSRES_LIG #include posre_npd.itp #endif ; Include water topology #include amber99sb.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic ion topology #include amber99sb.ff/ions.itp [ system ] ; Name system in water [ molecules ] ; Compound#mols A 1 B 1 NPD 1 SOL 42322 NA 24 The Protein and the Ligand were under energy minimization and a short MD separatedly to be sure there is no problem with the topology. But when I merge two topol.top from protein and from ligand, the error came at NPT step after successfully energy minimization and NVT This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. This is NPT.mdp title = system in water define = -DPOSRES -DPOSRES_LIG ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 50; 2 * 50 = 1000 ps, 1 ns dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 1.0 ps nstvout = 5000 ; save velocities every 1.0 ps nstenergy = 500 ; save energies every 1.0 ps nstlog = 500 ; update log file every 1.0 ps energygrps = Protein NPD ; Bond parameters continuation= yes ; Restarting after NVT constraint_algorithm= lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ;
[gmx-users] Umbrella Samling Alteration
Dear Gromacs Users I am currently running the series of simulations using the following command: mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg I wish to lessen the amount of time for each of these simulations from 10 ns to 6 ns. These simulations are already up to around 5 ns, is it possible to change the time to 6 ns without altering the md_umbrella.mdp file and starting agin? Also, will this reduction have any major impacts on the quality/efficacy of the data? Many Thanks, Alex This email may be confidential and subject to legal privilege, it may not reflect the views of the University of Canterbury, and it is not guaranteed to be virus free. If you are not an intended recipient, please notify the sender immediately and erase all copies of the message and any attachments. Please refer to http://www.canterbury.ac.nz/emaildisclaimer for more information. -- 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] template.cpp compilation problem with Gromacs 5.0.4
Dear Gromacs users I would like to code my own analysis programs but I'm facing problems with template.cpp compilations with gromacs 5.0.4. Made source GMXRC. cmake goes nicely but make does not make it. Any suggestions? downgrade? Here goes cmake and make output. Thanks a lot Milton $mkdir build $cd build $ cmake .. -- The C compiler identification is GNU 4.8.2 -- The CXX compiler identification is GNU 4.8.2 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Found PkgConfig: /usr/bin/pkg-config (found version 0.26) -- checking for module 'libgromacs' -- found libgromacs, version 5.0.4 -- Looking for GromacsVersion in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; -- Looking for GromacsVersion in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; - found -- Looking for init_mtop in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; -- Looking for init_mtop in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; - found -- Looking for output_env_done in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; -- Looking for output_env_done in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; - found -- Looking for gmx_nonbonded_setup in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; -- Looking for gmx_nonbonded_setup in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; - found -- Looking for init_domdec_vsites in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; -- Looking for init_domdec_vsites in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; - found -- Boost version: 1.55.0 -- Found GROMACS: /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so GROMACS version 5.0.0 found -- Configuring done -- Generating done -- Build files have been written to: /home/milton/pesq/bta/progs/template/build $make Scanning dependencies of target template [100%] Building CXX object CMakeFiles/template.dir/template.cpp.o In file included from /usr/local/gromacs/include/gromacs/analysisdata/modules/histogram.h:49:0, from /usr/local/gromacs/include/gromacs/analysisdata.h:209, from /usr/local/gromacs/include/gromacs/trajectoryanalysis.h:279, from /home/milton/pesq/bta/progs/template/template.cpp:38: /usr/local/gromacs/include/gromacs/analysisdata/modules/../../utility/uniqueptr.h:81:12: error: ‘std::move’ has not been declared using std::move; ^ /usr/local/gromacs/include/gromacs/analysisdata/modules/../../utility/uniqueptr.h:85:13: error: ‘unique_ptr’ in namespace ‘std’ does not name a type typedef std::unique_ptrT type; ^ In file included from /usr/local/gromacs/include/gromacs/analysisdata.h:209:0, from /usr/local/gromacs/include/gromacs/trajectoryanalysis.h:279, from /home/milton/pesq/bta/progs/template/template.cpp:38: /usr/local/gromacs/include/gromacs/analysisdata/modules/histogram.h:249:9: error: ‘type’ in ‘struct gmx::gmx_unique_ptrgmx::AbstractAverageHistogram’ does not name a type typedef gmx_unique_ptrAbstractAverageHistogram::type ^ /usr/local/gromacs/include/gromacs/analysisdata/modules/histogram.h:283:9: error: ‘AverageHistogramPointer’ does not name a type AverageHistogramPointer resampleDoubleBinWidth(bool bIntegerBins) const; ^ /usr/local/gromacs/include/gromacs/analysisdata/modules/histogram.h:295:9: error: ‘AverageHistogramPointer’ does not name a type AverageHistogramPointer clone() const; ^ In file included from /usr/local/gromacs/include/gromacs/options/basicoptions.h:54:0, from /usr/local/gromacs/include/gromacs/options.h:149, from /usr/local/gromacs/include/gromacs/trajectoryanalysis.h:280, from /home/milton/pesq/bta/progs/template/template.cpp:38: /usr/local/gromacs/include/gromacs/options/abstractoption.h:73:9: error: ‘type’ in ‘struct gmx::gmx_unique_ptrgmx::AbstractOptionStorage’ does not name a type typedef gmx_unique_ptrAbstractOptionStorage::type ^ /usr/local/gromacs/include/gromacs/options/abstractoption.h:123:17: error: ‘AbstractOptionStoragePointer’ does not name a type virtual AbstractOptionStoragePointer createStorage() const = 0; ^ In file included from /usr/local/gromacs/include/gromacs/options.h:149:0, from /usr/local/gromacs/include/gromacs/trajectoryanalysis.h:280, from /home/milton/pesq/bta/progs/template/template.cpp:38: /usr/local/gromacs/include/gromacs/options/basicoptions.h:101:17: error: ‘AbstractOptionStoragePointer’ does not name a type virtual AbstractOptionStoragePointer createStorage() const;
Re: [gmx-users] Force field For Protein-Ligand Complex
You may also use Amber99sb-ildn and GAFF for protein and ligand, respectively. You can find method in this paper: http://pubs.acs.org/doi/full/10.1021/ci500020m. Although, AM1-BCC method was used for charge calculations, I would suggest to use RESP method. With best regards, Rajendra -- 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] Using g_mindist for calculating hydrophobic interaction between protein and ligand
On 2/2/15 9:52 PM, Agnivo Gosai wrote: Dear Users I wish to characterize the hydrophobic interactions between a protein and a ligand by using the g_mindist analysis tool. I searched the forum and found a post which tells that it is supposedly the best tool available in gromacs for doing the job. Now , while reading the post a doubt cropped up in my mind. Do I need to provide an index file containing only the hydrophobic residues of the protein and the ligand ? Not just that, but just the hydrophobic atoms. Generally contact analysis focuses on heavy atoms, because hydrogens often inflate the totals. Or, just a normal index file with all the protein residues and ligand residues in two separate groups will do the job? No, this would give you the total number of atomic contacts between the protein and ligand, which is not what you're after. -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] Using g_mindist for calculating hydrophobic interaction between protein and ligand
Dear Users I wish to characterize the hydrophobic interactions between a protein and a ligand by using the g_mindist analysis tool. I searched the forum and found a post which tells that it is supposedly the best tool available in gromacs for doing the job. Now , while reading the post a doubt cropped up in my mind. Do I need to provide an index file containing only the hydrophobic residues of the protein and the ligand ? Or, just a normal index file with all the protein residues and ligand residues in two separate groups will do the job? Thanks Regards Agnivo Gosai Grad Student, Iowa State University. -- 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] combine two solvent box to one large box.
Hi, Strip the solvent, then you can use editconf to put the origin of both boxes at (0,0,0), then translate one of them, then use a text editor to put everything in the same coordinate file (updating atom counts and box vectors). Then solvate. Doing this on a solvated system is the path to the Dark Side... Mark On Mon, Feb 2, 2015 at 3:12 PM, BIRD vgsplay...@163.com wrote: hello all I have made two solvent boxes with DIFFERENT protein in each box, the box have the same X-Y-Z length. I want to combine two boxes to one large box at one dimension like X or Y Witch command could do that?? best regard Cao, PhD Institute of Physics Nankai University Tianjin, China -- 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] Problem with Lysozyme in Water Tutorial
On 2/2/15 12:10 PM, Stephen P. Molnar wrote: I have installed v-5.0.4 in Debian Wheezy without any warning or erroe messages. I have tried running the Lysozyme in Water Tutorial ( the one written for v-5) and have generated an error message in Step 4. The message is: File input/output error: ions.mdp For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I checked the reference and did not find one [defaults] directive in the .itp file, let alone two Pleas advise. You don't have ions.mdp in the working directory. -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] Problem with Lysozyme in Water Tutorial
I have installed v-5.0.4 in Debian Wheezy without any warning or erroe messages. I have tried running the Lysozyme in Water Tutorial ( the one written for v-5) and have generated an error message in Step 4. The message is: File input/output error: ions.mdp For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I checked the reference and did not find one [defaults] directive in the .itp file, let alone two Pleas advise. Thanks in advance. -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and Multivariate www.FoundationForChemistry.com (614)312-7528(c) Skype: smolnar1 -- 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 with Lysozyme in Water Tutorial
It just means you either missed grompp -f ions.mdp ... OR the ions.mdp file is not there in the directory where you are performing your simulations. On Mon, Feb 2, 2015 at 12:10 PM, Stephen P. Molnar s.mol...@sbcglobal.net wrote: I have installed v-5.0.4 in Debian Wheezy without any warning or erroe messages. I have tried running the Lysozyme in Water Tutorial ( the one written for v-5) and have generated an error message in Step 4. The message is: File input/output error: ions.mdp For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I checked the reference and did not find one [defaults] directive in the .itp file, let alone two Pleas advise. Thanks in advance. -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and Multivariate www.FoundationForChemistry.com (614)312-7528(c) Skype: smolnar1 -- 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] Hope this can help someone using REMD in Gromacs
Dear Gromacs User: I found when after running REMD in gromacs and try to generate trajectories for each replic based on the origin trajectories based on conditions, if the exchange step is mower than 1ps, after time pint 100ns there will be some noise spikes in the RMSD or other characters calculated from trajectories for each replic. The noise seems because when using demux.pl, the output formart for time is -20%g so you will get things like 399988 0 399988 1 399988 0 in your replica_index.xvg. If you want to remove the noise, you can 1) add a line $timestep = XXX; in beginning (XX is timestep with unit ps) 2) change print formart in line 33 and 44 from %-20g to %-20f 3) change the line 70 to $tstep = $log_time[4] * $timestep; Note the results based on origin demux.pl is CORRECT, it just a little noise. Hope this can help someone using REMD. Cheers: ) ZhiGuang Jia -- 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] Force field For Protein-Ligand Complex
Hello All I have to perform molecular dynamics simulation of protein-ligand complex in water. Initially I tried using gromos force field but there is some problem in its ligand itp file which is generated by PRODRG server. I also tried it with the help of ATB but again its giving error. Can I use CHARMM 27 or Charmm 36 force field for the same. Is there any reference paper?? Please help. With Regards Neha Bharti -- 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] DNA-protein complex - which force field to use?
Hi Jernej I'll choose AMBER or CHARMM, because these two forcefields have a more reliable description of nucleic acids. In my experience, OPLS-aa and GROMOS do not seem to be able to produce stable simulations in the large time scale for nucleic acids systems. Best regards Paulo Netz 2015-02-02 2:53 GMT+01:00 Jernej Zidar jernej.zi...@gmail.com: Hi everyone! I would like to study a DNA-protein complex. The protein part is composed of aminoacids covalently attached to the DNA bases. Which force field would you recommend? Based on recent experience I was thinking of using either OPLS-aa or CHARMM. OPLS-aa would be the prefered choice because it performs way better than CHARMM. Any recommendations or experiences? Thanks in advance! Jernej -- 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] Compilation errors (5.0.4)
Dear All, I am trying to compile Gromacs 5.0.4 on a CPU / GPU cluster and the details are as follows: Intel compiler (12.1), Cuda 4.2, MKL Library, single, GPU =on and however unable to compile. Please see the attached file for compilation details and errors / warnings: The errors in the 'make install' stage is listed below: CMake Error at src/programs/cmake_install.cmake:42 (file): file INSTALL cannot find /export/home/satya/gromacs-5.0.4/build-intel-mkl-cuda/bin/gmx. Call Stack (most recent call first): src/cmake_install.cmake:38 (include) cmake_install.cmake:48 (include) make: *** [install] Error 1 Kindly help. With best regards, Satyabrata Das -- 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.
