Applied Statistical Thermodynamics Universityof Natural Resources and LifeSciences Instituteof molecularmodeling and simulation Oostenbrink Chris Howand tosimulate using analyse GROMOS Applied Statistical Thermodynamics Schedule Applied Statistical Thermodynamics • • • Error messages Error of pentapeptide a simulations The tutorial: it to use need we what do and is GROMOS What – – How to analyse using gromos++ tools gromos++ using toanalyse How tools gromos++ using simulation up a to set How Outline Applied Statistical Thermodynamics • • • • • • • • Continueworking withit?Get alicense (max€200,-) room and upon request thiscourse for Binaries,force fieldsand partsof the manual available intraining the Lastestversion availableat: forcefields:GROMOS Functional libraryto easily implement newanalyses, algorithms, etc. Programlibrary for pre-and post-md: Simulationprogram: GRO ningen GROMOSsimulationsoftware MO lecular gromosXX, md++ 45A4, 53A6,54A7 S imulation package www.gromos.net gromos++, variousgromos++, programs Applied Statistical Thermodynamics Aprotocol basic very MDfora study solvation, solvation, energy minimisation in energyvacuum minimisation in coordinates, topology energy the of solvent minimisation trajectory analysis MD: production MD: equilibration adding ions
gromos++ gromos++ gromos md++ gromos Applied Statistical Thermodynamics Simulatingmolecular dynamicsusing topology GROMOS
configuration MDengine trajectories
inputfile Applied Statistical Thermodynamics
• • • • • /mms/common/gromos_20150304/gromosXX/BUILD.train/doc/index.html /mms/common/gromos_20150304/gromos++/BUILD.train/doc/index.html engine and the gromos++ programs at: programs gromos++ the and engine the MD- for find documentation can you room, Inthe training type: then line and command the flags from the input file corresponding with write an can Inyou addition, You typing: by line the from command the all programs run can @) by flags (preceded of input use make Programs post-MD and pre- MD-engine, available, programs Many program @finput_file.arg program @X ...@Y UsingGROMOS MD, keeps a record a keeps MD, post- and pre- for better checks quick for useful Applied Statistical Thermodynamics gromos++ documentation
Applied Statistical Thermodynamics • • • • • • • • specific programs only… programs specific by required thatare flags input course of are there And then @vector @atoms @props @pos @traj @topo flags: input Some common
GROMOS filename filename filename filename filename filename filename md Applied Statistical Thermodynamics • nonbonded interactions nonbonded field parameters force the and molecule your about information topological contains exclusions Lennard-Jones parameters atomic masses,charges Moleculartopology, @topo + H H N H H C bonded interactions bonded H C force constant dihedralangle phaseshift, multiplicity, bondangles, forceconstants bondlengths, forceconstants improper dihedrals, force constant O O - + H H N H C C O O - Applied Statistical Thermodynamics • • • • file. in stored are etc. types bond atom to types, the corresponding parameters The real types. by described etc. are Inthe *.mtbbonds atoms, file the block in the stored are blocks Building programs. GROMOS++ using together sugars,...) appropriate Topologies the joining by generated are of biomolecules ( *.mtb + N H Moleculartopology, @topo 3 H ) file. ) building blocks blocks building C H C O O - the interaction function parameter parameter function the interaction (amino acids, nucleotides, nucleotides, acids, (amino molecular topology building building topology molecular NH3+ GLY COO- ( *.ifp ) ) END [...] OA OM O names type # atom TYPE: 53 NRATT:# Waalsder van types atom of number ATOMTYPENAME END 2.0 TOPVERSION END [...] 0.0635078 PI) H/(2* = HBAR constant Planck's HBAR: # 138.9354 1.0/(4.0*PI*EPS0) FPEPSI: # PHYSICALCONSTANTS END 53a6.ifp 53a6.mtb MAKE_TOPtopology, using: TITLE Applied Statistical Thermodynamics GROMOS files make use of a block structure of a use block files make GROMOS Exampletopology file [...] B0 CHB CB # 52 types bond NBTY: # covalent of number BONDSTRETCHTYPE END [...] INE14 # # INE ATNM CGC CG PANM MRES MASS IAC atoms solute numberof NRP: # SOLUTEATOM END GLY # names residue AANM: 1 molecule solute a in residues of number NRAA2: # RESNAME 8 1.23000e+07 2.92273e+05 1.09000e-01 2.92273e+05 1.23000e+07 1.00000e-01 3.74000e+05 1.87000e+07 1.00000e-01 3.14000e+05 1.57000e+07 5 4 3 3 0 0.24800 1.00800 21 H2 1 2 5 4 3 2 4 0 0.24800 1.00800 21 H1 1 1 1 6 1 6 1 Applied Statistical Thermodynamics • • • • Example: Example: modelling the from be obtained can atom atoms, names) of file (number topology GROMOS to the must correspond x, x, y, coordinates z END BOX END POSITION END GLY NH3+ COO- TITLE 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.220300000 -0.129600000 GLY1 -0.137900000 8 O2 -0.014100000 -0.180300000 GLY1 -0.187600000 7 O1 0.090400000 -0.072700000 -0.186700000 GLY1 6 C 0.046000000 GLY 1 0.041300000 -0.093200000 5 CA -0.155398330 0.027294407 GLY1 -0.143271340 4 H3 -0.085700000 0.099000000 -0.142600000 GLY1 3 N -0.073884783 0.134539400 GLY1 -0.235321905 2 H2 0.173041108 GLY1 -0.081898071 1 -0.114565033 H1 Molecularconfiguration, @conf of each atom molecule in the of each data banks banks data solvation of solvation the addingcounterions...molecule, (PDB, NDB,...) or by NDB,...) by or (PDB, Applied Statistical Thermodynamics • • you can open in a web browser at browser in web a open can you which documentation, generated Doxygen in described are Blocks ( of blocks Consists GROMOS@inputinput file, • • • • • check the topology using the using topology the check ( molecules cyclic ( bridges for disulfide flags special acids amino of the states protonation the consider groups, terminal the define proper called is blocks building file the from topology the that generates program The gromos++ file parameter of the blocks inthe building defined are the pentapeptide todescribe needed The parameters make_top 1. Topology 1. ofthepentapeptide @solv H2O @seq NH3+VALTYR ARG LYSH GLNCOO- @param @build 54a7.ifp 54a7.ifp @cyclo > 54a7.mtb make_top peptide_54a7.top ) check_top check_top @cys 54a7.mtb ), heme groups ( groups heme ), program file and in the file and @heme ), ), Applied Statistical Thermodynamics 5. 2. 1. • • Prepare a topology that also contains the Cl- ions Cl- the contains that also topology a Prepare ions Cl- two with pentapeptide of the charge 2+ the Neutralize check the topology using the using topology the check com_top the program using ion the Cl- and of the files pentapeptide topology the combine program the file using of Cl- aion topology molecular a build 1. Topology: 1. adding counter ions @solv 1 @param 1 @topo com_top peptide_54a7.dat : check_top > peptide_2Cl_54a7.dat program 2: Cl_54a7.dat make_top Applied Statistical Thermodynamics # residue in topology atom in pdb atom in topology ATOMS END # name in my pdb name in topology RESIDUES END Library file to specify residue and atom names TITLE • • • Conversion to GROMOS format using program format toGROMOS Conversion format inPDB oftenavailable ofproteins Coordinates Order of atoms in pdb file do not have to match the topology the file donothavetomatch in pdb of atoms Order ILE ALA pdb2g96 – – Library file for non-standard names ( names non-standard file for Library names andatom viaresidue Identification CYS CYSH LYS LYSH > > @topopeptide_54a7.dat pdb2g96_peptide.g96 2. Coordinates 2. CB1 CB CD1 CD @lib @pdb @pdb peptide.pdb pdb2g96.lib pdb2g96 ): Applied Statistical Thermodynamics Warning: Couldnot find atom 22 (HH12), inresidue 3(ARG). Warning: Couldnot find atom 21 (HH11), inresidue 3(ARG). Warning: Couldnot find atom 18 (HE),inresidue 3(ARG). Warning: Couldnot find atom 12 (H),inresidue 3(ARG). • • • even if there are many,are if there even the warnings! at look should one messages: warning typical pdb2g96 – – places any the missing atoms at the origin (0.0 0.0 0.0) (0.0 0.0 origin at the atoms the missing any places the pdb-file in atoms unexpected skips Set coordinates to (0.00.00.0) Set coordinates to (0.0 0.00.0) Set coordinates to (0.0 0.00.0) Set coordinates to (0.0 0.00.0) 2. Coordinates 2. Applied Statistical Thermodynamics • • • Typical step: next Program structures in the X-ray seen often not are atoms Hydrogen – – – Slightly adjust coordinates to the coordinates Slightly adjust molecule in the strain Removes minimization Energy gch gch gch can calculate reasonable coordinates forthem coordinates reasonable calculate can @tol 0.1 @coord pdb2g96_peptide.g96 @topo peptide_54a7.dat 2. Coordinates 2. ofthe structure > force field force gch_peptide.g96 that is thatis used Applied Statistical Thermodynamics • • • • Typical step: next program the using molecule the Solvate conditions boundary on (periodic) Decide solvent in explicit molecules our We to like simulate typically > – – sim_box Removes strain in the solvent and solute-solvent interactions solute-solvent and solvent in the strain Removes minimization Energy simbox_peptide.g96 @minsol 0.23 @minwall 0.8 @solvent spc.g96 @solute gch_peptide.g96 @pbc r @topo peptide_54a7.dat 3. Solvation 3. of the solvent, keeping the solute fixed solute the keeping ofthe solvent, minimum solvent-solute distance minimum solutewall to distance rectangular boxshape sim_box Applied Statistical Thermodynamics • • • Alternatively, molecules water random select just also can we program using ions Cl- by potential electrostatic highest with the molecules water Replace box simulation to the ions Wecounter to add want may ion @coord peptide_h2o.g96 @mindist 0.35 @potential 0.8 @negative 2CL- @pbc r @topo peptide_54a7.top > peptide_2Cl_h2o.g96 ion 4. Ions 4. : minimum distance betweenions potential for cutoff calculation Applied Statistical Thermodynamics • • • • Open this in this Open out file a writes This to pdb back ions and file with solvent coordinate our Convert format the pdb read can Visualization programs frameout 5. Visualize 5. theresulting structure @traj @outformat @include @pbc pymol pymol @topo or FRAME_00001.pdb pdb ALL r vmd peptide_2Cl_h2o.g96 peptide_2Cl_54a7.dat note the differenttopology Applied Statistical Thermodynamics mk_script • • • release position restraints restraints position release to set aof simulations create Will Program together topology, simulation, MD the For come inputs the and coordinates @joblist equilibration.jobs @template mkscript.lib @files @dir tutorial/peptide/eq @bin /mms/common/gromos_20150304/gromosXX/BUILD. posresspec peptide_2Cl_h2o.posres coord input eq.imd topo @sys eq_peptide mk_script ... peptide_2Cl_54a7.dat peptide_2Cl_h2o.g96 6. MD 6. simulation helps you to prepare a simulation package simulation a to prepare you helps on peptide on the heat up heat the system, and gradually and system, the Applied Statistical Thermodynamics • • • For NTC = 1 (no shake on solute) rather use DT = 0.0005. if NTC = 1in SHAKE block. large DT inSTEP block is set to 0.002, which isconsidered to be too 2. WARNING (1) Maybe NSM should be3977 ? But coordinate file has 12507 lines in POSITION block. system From topology and SYSTEM block, I calculate 12516 atoms in the 1. ERROR (1) • • typical error and warnings: and error typical mk_script In GROMOS the user is allowed to do silly things silly do to allowed is GROMOS user In the Warnings Errors – – It is your responsibility to consider if a warning is relevant for you! relevant is awarning if consider to responsibility your It is forward. science brings That have to be fixed, otherwise the simulation will not run not will simulation the otherwise fixed, be to have are mere suggestions. mere suggestions. are also does consistency checks on your input your on checks consistency does also 6. MD 6. simulation . Applied Statistical Thermodynamics • • • • • • version of the mk_script library to prepare the appropriately job to prepare library of the mk_script version a special use to need you to the job a queue, submit you When e.g. the to queue, a job submit and in to server aLog desktop your to on run will want not you simulations, Longer etc. (eq_peptide_2.run), job next the start automatically will At script this end, the scripts the Run generated that mk_script the scripts job with happy are you Once qsub –jeq_peptide_1.run –qstudent –c4 ./eq_peptide_1.run submit myjobto the‘student’ queue, use4CPUs 6. MD 6. simulation Applied Statistical Thermodynamics • • • • • • ... Distributions Correlations, solutions of Properties properties Energetic properties Structural in? interested typically we are properties What – – – – – – – – – diffusion viscosity density ... folding, of binding, free energy the system of components between energy interaction conformations of observed clustering analysis), (NOE experiments NMR with agreement from initial the structure deviations root-mean-square bonds of hydrogen occurence 7. 7. Analysis Applied Statistical Thermodynamics Selecting thepropergather method canbe quite achallenge! • • • • @pbc r cog reconstruct the molecule: gathering molecule: the reconstruct to it is important analyses, and some visualization For distances: calculate to convention image nearest the use programs Analysis boundary box the by to be split seem may The molecule used commonly are conditions boundary Periodic – – – Follow atom number, atom Follow the or bonds Take images nearest subsequent Take copy periodic closest the box shapegather method Boundariesand gathering 2 6 1 5 4 3 1 2 3 4 5 Applied Statistical Thermodynamics • • • Use the program program the Use Atomspecifiers an analysis for atoms specific to use need Often you atominfo s:OW 2:CA,1-7 1:O? 1:res(4:CA) 1:CA a:1,5 s:4-12 1:3-6,8 2:3 – – examples: examples: spaces!) (no string of one consists @atomspec 1:1-8,13 third atomofthe @topo peptide_2Cl_54a7.dat all“ atoms allatomswith anamestarting with“ allatomswith name“ atoms atoms OW CA atoms atominfo Atomspecifiers 1 1 3 ” atomsin” the atomsof residue to and , 4 , 5 7 4 , and all “ 6 second to 5 and of 12 to check what the atomspecifier does atomspecifier the what to check all of the 8 molecules molecule of the of CA CA solvent ” of molecule” of ” inmolecule solvent 4 inmolecule first molecule O ” inmolecule 2 1 1 1 Applied Statistical Thermodynamics rmsd • • • position for selected atoms for selected position fluctuations root-mean-square atom-positional Similarly, program configurations two between deviation of structural Measure deviations root-mean-square Atom-positional > @traj md_peptide_1.trj.gz @ref peptide_2Cl_h2o.g96 @atomsrmsd 1:CA,N,C @time 00.5 @pbc r – rmsd_peptide.out reference configuration: e.g. X-ray or NMR structure NMR or e.g.X-ray configuration: reference @topo peptide_2Cl_53a6.dat around the average the around md_peptide_3.trj md_peptide_2.trj 7. 7. Analysis:RMSD rmsf calculate the calculate atomsto consider for rmsd (RMSD) Applied Statistical Thermodynamics tser • Timethe by of different given series properties, @traj md_peptide_1.trj.gz @prop @time 00.5 @pbc r @topo peptide_2Cl_53a6.dat d%1:3,69 > md_peptide_3.trj.gz md_peptide_2.trj.gz t%1:47,46,48,49 a%1:70,69,71 7. 7. series time Analysis: tser_peptide.out angle distance torsional angle property specifier property Applied Statistical Thermodynamics hbond • • Defined using Defined bonds hydrogen of Weoccurrence the monitor can – – – > @trajmd_peptide_1.trj.gz 135 0.25 @Hbparas mass.file @massfile @AcceptorAtomsB2:a 2:a @DonorAtomsB @AcceptorAtomsA1:a 1:a @DonorAtomsA 0.5 0 @time r @pbc – H...acceptor distance maximally 0.25 nm 0.25 maximally distance H...acceptor e.g.: criteria, geometric acceptors and donors the for atomspecifiers the donor...H...acceptor minimally135° angle hbond_peptide.out @topo peptide_2Cl_54a7.dat @topo 7. 7. Analysis:Hydrogen bonds between molecules 1and2 between molecules allbonds hydrogen us this gives filters for relevant atoms filters for Applied Statistical Thermodynamics • bonds in a DNA-ligand complex in DNA-ligand a bonds Watson-Crickthe monitoring Example: hydrogen 7. 7. Analysis:Hydrogen bonds Applied Statistical Thermodynamics rmsdmat •. 1. • • writes the output file output the writes analysis clustering, matrix, ofan rmsd calculation steps: three configurations generic aof set onto simulations the during sampled the map structures trajectory file: trajectory in a of structures pairs all between deviation root-mean-square program gromos++ @traj md_peptide_1.trj.gz @stride 1 @atomsfit 1:CA,N,C @pbc r 7. 7. structuralclustering Analysis: @topo peptide_2Cl_54a7.dat md_peptide_3.trj.gz md_peptide_2.trj.gz rmsdmat.bin rmsdmat.bin rmsdmat calculates the atom-positional atom-positional the calculates (large file) (large Applied Statistical Thermodynamics cluster 4. 2. analysis on the output ofthe output on the analysis program gromos++ rmsdmat.bin. matrix, the similarity on based clustering program gromos++ – – – – – Mark cross clustering over multiple trajectories over clustering cross Mark clusters into the trajectories Filtering of analysis Life-time etc. structures, representative of clusters, number sizes, cluster with output Gives cluster part same of the cutoff the than smaller RMSD are with The structures @time 00.5 @cutoff 0.1 7. 7. structuralclustering Analysis: @rmsdmat @rmsdmat RMSDMAT.bin postcluster cluster performs conformational conformational performs cluster can do additional additional do can program Applied Statistical Thermodynamics density =MASS/ boxvol boxvol =VOLUME[1] totpot =ENER[3] totkin =ENER[2] totene =ENER[1] time =TIME[2] # program ene_ana. # whichisspecified by theinputflag en_files of # blockdefinition for theenergy trajectory file. ENERTRJ END TITLE • • • XX Library file for ene_ana the properties are defined in the library in the library defined are the properties trajectories the from energy program analysis later for files trajectory to separate energies (free) write can GROMOS 7. 7. ofenergies time-series Analysis: ene_ana extracts time series of different time series properties extracts ENER this identifies e.g. the second value in the blockto thevariable ene_ana.md++.lib totkin Applied Statistical Thermodynamics ene_ana • • density.dat totkin.dat totpot.dat to files time series and Writesto output, summary the Use totene.dat 7. 7. ofenergies time Analysis: series @en_files md_peptide_1.ene.gz @lib ene_ana.md++.lib @prop totene totpot totkin density @time 00.5 ene_ana > @topo peptide_2Cl_53a6.dat ene_ana_peptide.out program together with the library file library with the together program md_peptide_3.ene.gz md_peptide_2.ene.gz Applied Statistical Thermodynamics • • • • • • • Did you make manual changes to the topology or the trajectory? the or to the topology changes manual make you Did did help? all not This again(!) input, your Check coordinates with the in combination topology your Check topology your Check input your Check the message Read – – – – can other programs read this combination? this read programs other can one? the correct using you are file names) atomspecifiers, files,to the paths input flags, to you? anything it mean does Maybe something is wrong with the program. Catch the bug! the Catch program. with the is wrong something Maybe 8. Error messages 8. dangerous, try to avoid try dangerous, Applied Statistical Thermodynamics • • • • Advanced user Advanced GROMOS with not but Someexperience, beginner Complete before computer a used Never – – – – – – Maybe there is a specific technique that you want want to learn? that you technique specific is a there Maybe things own your try Then GROMOS in work things to findout the Start how tutorial with tutorial the /extend simulation own your up to try set Then it how works time to understand your the take Start tutorial, with environment with linux a computer a getting to Start use with Don’t be afraid of the programs or the computers. computers. the or programs the of afraid be Don’t Try experience! get and works what out Finalremark