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- 1. GROMACSTutorial GROMACSIntroductoryTutorial Gromacsver3.3.1
Author: JohnE.Kerrigan,Ph.D.
AST/IST,UniversityofMedicineandDentistryofNJ 675HoesLane
Piscataway,NJ08554 Phone: (732)2354473 Fax: (732)2355252 Email:
kerrigje@umdnj.edu 1
- 2. GROMACSTutorial
GROMACSTutorialforSolvationStudyofSpiderToxinPeptide.
Yu,H.,Rosen,M.K.,Saccomano,N.A.,Phillips,D.,Volkmann,R.A.,Schreiber,S.L.:
SequentialassignmentandstructuredeterminationofspidertoxinomegaAgaIVB.
Biochemistry32pp. 13123(1993)
GROMACSisahighend,highperformanceresearchtooldesignedforthestudyofprotein
dynamicsusingclassicalmoleculardynamicstheory.[1]
ThisversatilesoftwarepackageisGnu
publiclicensefreesoftware.Youmaydownloaditfrom
http://www.gromacs.org .GROMACS
runsonlinux,unix,andonWindows(arecentdevelopment).
Synopsis.Inthistutorial,youwillstudyatoxinisolatedfromthevenomofthefunnelwebspider.
Venomtoxinshavebeenusedinthepasttoidentifycationchannels.Calciumionchannelsregulate
theentryofthisionintocells.Nervesignalsarehighlygovernedbythebalanceofionsinneuronal
cells.Itishypothesizedthatexposedpositivelychargedresiduesinvenomslikethespidertoxin
herebindfavorablytothenegativelychargedentranceofthecellsionchannel.Thespidertoxinin
thistutorialhasitspositivelychargedresiduespointingpredominantlytoonesideofthepeptide.
Theionchannelisblocked,resultinginblockednervesignalleadingtoparalysisandultimatelyto
death(presumablyviarespiratoryfailure).
Wewillstudythispeptidetoxinusingexplicitsolvationdynamics.First,wewillcompareanin
vacuomodeltoasolvatedmodel.Wewillsolvatethepeptideinawaterboxfollowedby
equilibrationusingNewtonslawsofmotion.Wewillcompareandcontrasttheimpactof
counterionsintheexplicitsolvationsimulation.Wewillseekanswerstothefollowingquestions:
Isthesecondarystructurestabletothedynamicsconditions?
Arethesidechainsofthepositivelychargedresiduespredominantlydisplacedtoonesideofthe
peptidestructure?Dothecounterionsholdthesepositivelychargedresiduesin
placeordothey movearound?
Whatroledoeswaterplayinmaintainingthestructureofproteins?
Note:Youwillgenerategromacs(*.gro)structurefilesinthistutorial.Toviewthesefiles,you
mustuseVMD(Downloadfrom:http://www.ks.uiuc.edu/Research/vmd/).
Inaddition,you shouldobtainacopyoftheGROMACSusermanualat
http://www.gromacs.org .
Download1OMB.PDBfromtheProteinDataBank(http://www.rcsb.org/pdb/).
ItisadvisabletouseDeepView(DownloadDeepViewfrom
http://www.expasy.ch/spdbv/) to
previewthefileifyouknowthatyourstructuremaybedisordered(i.e.residueswithmissingside
chains).DeepViewwillreplaceanymissingsidechains(However,bewareasDeepViewwillmark
thoserebuiltsidechainswithastrangecontrolcharacterthatcanonlyberemovedmanuallyusinga
2
- 3. GROMACSTutorial texteditor!).
Therearenomissingsidechainsinthispdbfile,sowewillnotworryaboutthatin
thisexercise.
Createasubdirectoryinyourunixaccountcalledfwspider.Withinthisnewdirectory,createthe
followingdirectories:invacuo,wet,andionwet.Usesftptocopythe1OMB.pdbfiletothe
fwspidersubdirectories(placeacopyineachsubdirectorywithinthefwspiderdirectory).
(IMPORTANT!WheneveryousftpatextfiletoaunixsystemfromWindows,besuretoconvert
thefiletoaunixtextfile.Dothisusingtheto_unix command(e.g. to_unix
filenamefilename convertsfilename toaunixtextfile.
InRedHatLinux,usethedos2unix command. Texteditorsin
WindowslikeMSWordaddcontrolcharactersthatmaycauseerrorsinunixprograms.)
Processthepdbfilewith pdb2gmx.Thepdb2gmx
(toviewthecommandlineoptionsforthis commandjusttypepdb2gmx
hInfact,togethelpforanycommandinGromacsjustusetheh
flag)commandconvertsyourpdbfiletoagromacsfileandwritesthetopologyforyou.Thisfileis
derivedfromanNMRstructurewhichcontainshydrogenatoms.Therefore,weusetheignhflag
toignorehydrogenatomsinthepdbfile.Theffflagisusedtoselecttheforcefield(G43a1isthe
Gromos96FF,aunitedatomFF).Thef
flagreadsthepdbfile.Theoflagoutputsanewpdb
file(variousfileformatssupported)
withthenameyouhavegivenitinthecommandline.Thep
flagisusedforoutputandnamingofthetopologyfile.Thetopologyfileisveryimportantasit
containsalloftheforcefieldparameters(basedupontheforcefieldthatyouselectintheinitial
prompt)foryourmodel.
RecentstudieshaverevealedthattheSPC/Ewatermodel [2]performs
bestinwaterboxsimulations.[3]
Usethespcewatermodelasitisbetterforusewiththelong
rangeelectrostaticsmethods.So,weusethewaterflagtospecifythismodel.
pdb2gmx ignhff G43a1f 1OMB.pdb ofws.pdb pfws.topwater spce
SetuptheBoxforyoursimulations editconf btcubicffws.pdb ofws.pdb
d0.9
Whatyouhavedoneinthiscommandisspecifythatyouwanttouseasimplecubicbox.
Thed 0.9flagsetsthedimensionsoftheboxbasedupon
settingtheboxedgeapprox0.9nm(i.e.9.0
angstroms)fromthemolecule(s)periphery.Ideallyyoushouldsetdatnolessthan0.85nmfor
mostsystems.[4] [SpecialNote: editconf
mayalsobeusedtoconvertgromacsfiles(*.gro)topdbfiles(*.pdb)and
viceversa.Forexample:editconf f file.groo file.pdbconverts file.gro
tothepdbfilefile.pdb]
Youmayusethefilesgeneratedfromthethissteptobeginyourinvacuosimulation.Forthein
vacuoworkjustmoveaheadtotheenergyminimizationstepfollowedbythemoleculardynamics
step(Nopositionrestraineddynamicsnecessaryforinvacuowork.Why?).
SolvatetheBox genbox cpfws.pdb csspc216.groofws_b4em.pdb pfws.top
3
- 4. GROMACSTutorial Thegenbox
commandgeneratesthewaterboxbaseduponthedimensions/boxtypethatyouhad
specifiedusingeditconf.Inthecommandabove,wespecifythespcwaterbox.
Thegenbox
programwilladdthecorrectnumberofwatermoleculesneededtosolvateyourboxofgiven
dimensions. Setuptheenergyminimization.
Usetheem.mdpfile.Gromacsusesspecial*.mdpfilestosetup
theparametersforeverytypeof
calculationthatitperforms.Lookintothecontentsofthisfile.Itspecifiesasteepestdescents
minimizationtoremovebadvanderWaalscontacts.Editthefileandchangenstepsto400.Ifthe
minimizationfailstoconverge,resubmitwithnsteps=500.(Theminimizationshouldconvergein
lessthan400stepshowever,differentplatformsresponddifferently.)Toresubmitthejob,you
willneedtorerungrompp.(Note:thepathtothecpreprocessormaybedifferentonyour
machine.Usethewhichcommandtolocate[i.e.whichcpp]!) Contentofem.mdp:
title=FWS cpp= /usr/bin/cppthecpreprocessor define= DFLEXIBLE
constraints=none integrator =steep dt=0.002ps! nsteps=400
nstlist=10 ns_type=grid rlist=1.0 coulombtype=PME rcoulomb=1.0
vdwtype=cutoff rvdw =1.4 fourierspacing =0.12 fourier_nx =0
fourier_ny =0 fourier_nz =0 pme_order =4 ewald_rtol =1e5
optimize_fft =yes Energyminimizingstuff emtol=1000.0 emstep=0.01
Importantaspectsoftheem.mdpfile:
titleThetitlecanbeanygiventextdescription(limit64characterskeepitshortandsimple!)
cpplocationofthepreprocessor definedefinestopasstothepreprocessor.
DFLEXIBLEwill tellgrompptoincludetheflexible SPCwatermodel
insteadof therigidSPCintoyourtopology.Thisallowssteepestdescentsto
minimizefurther. 4
- 5. GROMACSTutorial constraintssetsanyconstraintsusedinthemodel.
integrator
steeptellsgromppthatthisrunisasteepestdescentsminimization.Usecgfor
conjugategradient. dt
notnecessaryforminimization.Onlyneededfordynamicsintegrators(likemd).
nstepsInminimizationruns,thisisjustthemaximumnumberofiterations.
nstlistfrequencytoupdatetheneighborlist.nstlist=10(updates
thelistevery10steps). rlistcutoffdistanceforshortrangeneighborlist.
coulombtype
tellsgromacshowtomodelelectrostatics.PMEisparticlemeshewaldmethod
(pleaseseetheGromacsusermanualformoreinformation).
rcoulombdistanceforthecoulombcutoff vdwtype
tellsGromacshowtotreatvanderWaalsinteractions(cutoff,Shift,etc.)
rvdwdistancefortheLJorBuckinghampotentialcutoff EMStuff emtol
theminimizationconvergeswhenthemaxforceissmallerthanthisvalue(inunitsofkJ
1 1 mol nm ) emstepinitialstepsize(innm). Nowprocessthefileswith
grompp. gromppisthepreprocessorprogram(thegromacspre
processorgromppGetit!Sigh!).
gromppwillsetupyourrunforinputintomdrun. gromppf
em.mdpcfws_b4em.pdb pfws.top ofws_em.tpr
Thefflagingromppisusedtoinputtheparameterfile(*.mdp).Thecflagisusedtoinputthe
coordinatefile(thepdbfile,*.pdb)
pinputsthetopologyandooutputstheinputfile(*.tpr) neededformdrun.
Usinggenionandthetprfiletoaddions.Youmayusethetprfilegeneratedheretoadd
counterionstoyourmodeltoneutralizeanynetcharge.Ourmodelhasanetchargeof+2.00.
Therefore,wewanttoaddtwochlorideions.Copythefws_em.tprfilethatyouusedforyour
explicitsolvatedmodeltoyourionwetsubdirectory.Inaddition,copyyourfws.topandposre.itp
filesfromyourexplicitsolvationmodeltoyourionwetsubdirectory.Usethegenioncommandto
addthechlorideions. genionsfws_em.tpro fws_ion.pdb nnameCLnn 2g
fws_ion.log
Wherennameisthenegativeionname(CLfortheGromosG43a1forcefieldseetheions.itp
fileforspecificswrtforcefield),nnisthenumberofnegativeionstoadd.Thegflaggivesa
nametotheoutputlogforgenion.
Whenyouprocessthiscommand,youwillbepromptedtoprovideacontinuousgroupofsolvent
molecules,whichshouldbeGroup12(SOL).Type12then.Youwillnoticethattwo
solventmoleculeshavebeenreplacedbyClions.Nowyoumustmakethefollowing
additions/correctionstoyourfws.topfile: Add 5
- 6. GROMACSTutorial #includeions.itp
(Note:Thisshouldbepresentbydefaultalreadyinversion3.2&greater)
aftertheincludestatementfortheforcefield.Subtract2fromthetotalnumberofSOLmolecules
andaddalinefor2Clmoleculesinthe[molecules]sectionattheendofthefile.Youwillalso
needtomodifythetemperaturecouplingschemeforyourpr_md.mdpandmd.mdpfiles.
Now,youwillusefws_ion.pdbinplaceoffws_b4em.pdbforgeneratingtheactualinputtpr
using gromppforenergyminimization.
Temperaturecouplingschemeforthepr_md.mdpandmd.mdpfilesafteraddingchlorideions.
Berendsentemperaturecouplingison Tcoupl=berendsen tau_t=0.1 0.1
tc_grps =protein nonprotein ref_t=300 300
Remember:Ifyouaddedthechlorideions,youwillneedtorunthegromppstepagain.
First removetheoldfws_em.tprfile,thenrunthenextgromppcommandbelow.
Weaddedchlorideions
inourmodeltoneutralizedtheoverallnetchargeofthemodel. gromppf
em.mdpcfws_ion.pdb pfws.top o fws_em.tpr
Runtheenergyminimizationinbackground(Usetheampersand&attheendofthecommand).
mdrunvdeffnm em (deffnm
tellsgromacsthedefaultfilenametousefortherun.Thisisaveryusefulshortcut.)
Usethetail commandtocheckontheprogressoftheminimization. tail
15em.log
Whentheminimizationiscomplete,youshouldseethefollowingsummaryinyourlogfile
indicatingthatsteepestdescentsconverged.Usetail 50em.log
SteepestDescentsconvergedtoFmax0.001ps). [7] Studythemdp filebelow.
Contentofpr.mdp. title=FWS warnings=10 cpp=/usr/bin/cpp define=
DPOSRES constraints=allbonds integrator =md dt=0.002 ps!
nsteps=10000 total20.0ps. nstcomm=1 nstxout=250
collectdataevery0.5ps nstvout=1000 nstfout=0 nstlog=10 nstenergy=10
nstlist=10 ns_type=grid rlist=1.0 coulombtype =PME rcoulomb=1.0
vdwtype=cutoff rvdw=1.4 fourierspacing =0.12 fourier_nx =0
fourier_ny =0 fourier_nz =0 pme_order =4 ewald_rtol =1e5
optimize_fft =yes Berendsentemperaturecouplingison Tcoupl=berendsen
tau_t=0.1 0.1 tcgrps =proteinnonprotein ref_t=300 300
Pressurecouplingison Pcoupl=parrinellorahman tau_p=0.5
compressibility=4.5e5 ref_p=1.0 Generatevelocitesisonat300K.
gen_vel=yes gen_temp=300.0 gen_seed =173529 7
- 8. GROMACSTutorial Importantthingstoknowaboutthemdpfile.
TheDPOSREinthedefinestatementtellsGromacstoperformpositionrestraineddynamics.
Theconstraintsstatementisaspreviouslydiscussed.
allbondssetstheLINCSconstraintforall bonds.[7] Theintegrator
tellsgromacswhattypeofdynamicsalgorithmtouse(anotheroptionissdfor
stochasticdynamics).
dtisthetimestep(wehaveselected2fshowever,thismustbeenteredinunitsofps!).
nstepsisthenumberofstepstorun(justmultiplynstepsXdttocomputethelengthofthe
simulation).
nstxouttellsgromacshowoftentocollectasnapshotforthetrajectory.(e.g.nstxout=250with
dt=0.002wouldcollectasnapshotevery0.5ps)
coulombtypeselectsthemannerinwhichGromacscomputeselectrostaticinteractionsbetween
atoms.(PMEisparticlemeshewaldthereareotheroptionslikecutoff).
rcoulombandrvdwarethecutoffs(innm1.0nm=10.0angstroms)fortheelectrostaticandvan
derWaalsterms.
Thetemperaturecouplingsectionisveryimportantandmustbefilledoutcorrectly.
Tcoupl =berendsen
[8](typeoftemperaturecouplinganotheroptionisnosehoover)
tau_t=Timeconstantfortemperaturecoupling(units=ps).Youmustlistoneper
tc_grpinthe orderinwhichtc_grpsappear.
tc_grps=groupstocoupletothethermostat(everyatomorresidueinyourmodelmustbe
representedherebyappropriateindexgroups).
ref_t=referencetemperatureforcoupling(i.e.thetemperatureofyourMDsimulationindegrees
K).Youmustlistonepertc_grpintheorderinwhichtc_grpsappear.
Whenyoualterthetemperature,dontforgettochangethegen_tempvariableforvelocity
generation. pcoupl istheParrinelloRahmanbarostat.
pcoupltypeisotropicmeansthattheboxwillexpandorcontractevenlyinalldirections(x,y,
andz)inordertomaintaintheproperpressure.
Note:Usesemiisotropicformembranesimulations. tau_p
timeconstantforcoupling(inps). 1
compressibilitythisisthecompressibilityofthesolventusedinthesimulationinbar
(the settingaboveisforwaterat300Kand1atm).
ref_pthereferencepressureforthecoupling(inbar)(1atm~0.983bar).
8
- 9. GROMACSTutorial Preprocessthepr.mdpfile. gromppf
pr.mdpcem.grop fws.top opr.tpr nohupmdrundeffnm pr& Usethetail
commandtocheckthepr.logfile. Themd.mdpparameterfilelooksvery
similartothepr.mdpfile.Thereareseveraldifferences.
Thedefinestatementisnotnecessaryaswearenotrunningaspositionrestraineddynamics.
Contentofmd.mdpforexplicitsolvation
(SpecialNote:Forinvacuo,removetheentriesforsol
inthetemperaturecouplingsection.Forthesimulationthatincludesthecounterions,addanentry
fortheionsinthetemperaturecouplingsection.) title=FWS
cpp=/usr/bin/cpp constraints=allbonds integrator=md dt=0.002 ps!
nsteps=25000 total50ps. nstcomm= 1 nstxout=500 collectdataevery1ps
nstvout=0 nstfout=0 nstlist=10 ns_type=grid rlist=1.0 coulombtype
=PME rcoulomb=1.0 vdwtype =cutoff rvdw=1.4 fourierspacing =0.12
fourier_nx =0 fourier_ny =0 fourier_nz =0 pme_order =4 ewald_rtol
=1e5 optimize_fft =yes Berendsentemperaturecouplingison
Tcoupl=berendsen tau_t =0.1 0.1 tcgrps =protein nonprotein ref_t
=300 300 Pressurecouplingison Pcoupl=parrinellorahman tau_p=0.5
compressibility=4.5e5 ref_p=1.0 Generatevelocitesisonat300K.
gen_vel=yes 9
- 10. GROMACSTutorial gen_temp=300.0 gen_seed=173529
gromppfmd.mdpcpr.grop fws.top omd.tpr nohupmdrundeffnmmd&
Usethetail commandtocheckthemd.logfile.
Youmaycompressthetrajectoryusingtrjconvtosaveondiskspace.
trjconvfmd.trr omd.xtc
Onceyouhavemadethe*.xtcfile,youmaydeletethe*.trrfile. Usengmx
toviewthetrajectory(youmayalsodownloadtoyourPCanduseVMDtoviewthe
trajectory). ngmx fmd.trr(ormd.xtc)smd.tpr
Whentheviewercomesup,youwillseeadialogboxwithanumberofselections.Checkthebox
labeledProtein,thenclickOk. ngmxsinitialstartupdialog. 10
- 11. GROMACSTutorial
SelectingProteinpermitsustoviewtheproteinonlywithoutinterferencefromthe~3,000water
moleculesthatoccupytherestofthebox. UseXRotate
torotatetheboxupanddown(leftmouseclickgoesuprightmouseclickgoes
down).UseYRotate
torotatetheboxfromlefttorightorviceversa(leftmouseclickrotatesto
theleftandrightmouseclickrotatestotheright).
Scaleatthebottompermitsyoutozoominand
zoomout(useleftmousebuttontozoominandrightmousebuttontozoomout).
ToviewanothergroupinthemodelgotoDisplay>Filterandtheinitialdialogboxwillcome
upagainandyoumayopttoviewsomeotherindexgroup(e.g.thebackbone).
ToviewtheanimationoftheMDtrajectorygoto
Display>Animate.Controlsusedforthe
playbackofthetrajectoryappearatthebottomofthewindow.Usethecenterarrowbuttontoview
onetimestepattime.Usetheforwarddoublearrowtoplaythewholetrajectory,andusethe
pausebuttontotherighttostopthetrajectoryplayback.Usethedoublearrowtothelefttoreset
theanimation.
Unfortunately,thesaveaspdboptionundertheFilemenuinngmxdoesnotwork.Therefore
Thebestwaytoviewthetrajectoryandselectsnapshotstosaveas*.PDBfilesistousevisual
moleculardynamics(VMD).
(Downloadfrom:http://www.ks.uiuc.edu/Research/vmd/ Itsfreeto
academicsanditrunsonunixandwindows!). Analysis
OneofthemajoradvantagesofGromacs(otherthanthefactthatitisGNUpublicdomainand
free!)istherobustsetofprogramsavailableforanalyzingthetrajectories.Wewilldiscussafewof
themostimportantanalytictoolsintheGromacsarsenalhere. 11
- 12. GROMACSTutorial Groups make_ndx
Themake_ndxprogramisusefulforgeneratinggroups(IDtagsforspecificatomsorresiduesthat
youmaywanttoanalyze).Gromacsgeneratesdefaultgroupswhichmaybeadequateforyourwork
asis.However,ifyouneedtodomoreindepthanalysis,usemake_ndxtotagspecificitemsin
yourmodel.Seethemanualformoreinformation. Howtousemake_ndx
tosetupindex(ndx)files.Usemake_ndxtoidentifyparticulargroupsthat
youmightwanttofreezeduringasimulationorgatherspecialenergyinformation.Letslookatan
examplewherewewanttofreezetheNandCterminalaminoacidsofaprotein.Alwaysuse
make_ndxtocreateanindexgroupforusewiththegromppprogram.
Inthissamplecase,wehaveacoordinatefileofacollagentriplehelix,postpositionrestrained
dynamics,wherewewanttofreezetheN&Cterminalforproductionrun.Wemustfirstidentify
theresidue#sinthecoordinatefile(Inourcaseclg_b4md.pdb)thatidentifytheN&Ctermini.
Thecommandlineissimpleenough make_ndx f clg_b4md.pdb oclg_ter.ndx
Youwillseethefollowingoutput(weleftoutthedescriptiveinfoatthebeginning)followedbya
commandprompt(>). Readingstructurefile
Goingtoread0oldindexfile(s) Analysingresiduenames:
Openinglibraryfile/usr/share/gromacs/top/aminoacids.dat Thereare:
2194OTHERresidues Thereare:108PROTEINresidues Thereare:0DNAresidues
AnalysingProtein... AnalysingOther... 0System:7365atoms
1Protein:765atoms 2ProteinH:687atoms 3Calpha:108atoms
4Backbone:324atoms 5MainChain:435atoms 6MainChain+Cb:507atoms
7MainChain+H:477atoms 8SideChain:288atoms 9SideChainH: 252atoms
10ProtMasses:765atoms 11NonProtein:6600atoms 12DRG:21atoms
13SOL:6579atoms 14Other:6600atoms 12
- 13. GROMACSTutorial nr:group!'name'nrname'splitch'nr
Enter:listgroups 'a':atom&'del'nr'splitres'nr'l':listresidues
't':atomtype|'keep'nr'splitat'nr'h':help
'r':residue'res'nr'chain'char "name":group'case':casesensitive
'q':saveandquit >
UsethercommandtoenterthelistofresiduenumbersthatrepresenttheN&Cterminiofthe
triplehelix. >r136377273108 15r_1_36_37_72_73_108:51atoms
Note:Youmayalsouseadashtospecifyaresiduenumberrange(e.g.tospecifyresidues1to36
use>r136) Thedefaultname(r_1_36_37_72_73_108 )
givingtothenewindexgroupthatyouhavejust
creatediscumbersome.Letsrenameitusingthenamecommand.Wewillusetheindexgroup#
(15)inthecommand. >name15Terminal >v Turnedverboseon
0System:7365atoms 1Protein:765atoms 2ProteinH:687atoms
3Calpha:108atoms 4Backbone:324atoms 5MainChain:435atoms
6MainChain+Cb:507atoms 7MainChain+H:477atoms 8SideChain:288atoms
9SideChainH:252atoms 10ProtMasses:765atoms 11NonProtein:6600atoms
12DRG:21atoms 13SOL:6579atoms 14Other:6600atoms 15Terminal:51atoms
nr:group!'name'nrname'splitch'nrEnter:listgroups
'a':atom&'del'nr'splitres'nr'l':listresidues
't':atomtype|'keep'nr'splitat'nr'h':help
'r':residue'res'nr'chain'char
"name":group'case':casesensitive'q':saveandquit > 13
- 14. GROMACSTutorial
Weusedthevcommandtoverifythatournamechangewassuccessful.Tofinishup,usetheq
commandtosaveandquitandyouredone.
Nowhowdowefreezethegroups?Easy,addthefollowinglinestoyourmd.mdpfile
energygrps_excl=TerminalTerminalTerminalSOL!Toremove
computationofnonbondinginteractionsbetweenthefrozengroupswitheachother
andsurroundings(i.e.thesolvent,SOL) freezegrps
=Terminal!Indexgrouptofreeze freezedim =YYY
!Freezethisgroupinalldirections,x, y,andz
Remember,youmustincludethenewindexfilewhenyouusethismd.mdpfiletocreateyourrun
inputfile(tpr)usinggrompp.Usethenflagtogrompp.Forexample
gromppfmd.mdpcpr.grop clg.top n clg_ter.ndx omd.tpr Properties
g_confrms
TocomparethefinalstructuretotheoriginalPDBfileobtainedfromthePDBuseg_confrms(fora
descriptionuseg_confrmsh).Thisprogramtakestwostructuresandperformsaleastsquaresfit.
g_confrmsf11OMB.pdb f2md.groofit.pdb
Youwillbepromptedtoselectagroup(selecttheBackbone(group4)bothtimes).Theprogram
reportsanRMSdeviationandproducesanoutputfile(fit.pdb).Theoutputfilewillshowthetwo
structuressuperimposedon eachother. g_covar
Usetocomputethecovariancematrix(seemanualformoreinfo).Mayalsobeusedtocomputean
averagestructurefromadynamicstrajectory.Forexampletocomputetheaverageofthelast200
psofa1nsdynamicsrunuse g_covar f traj.xtcstopol.tprb 801e 1000av
traj_avg.pdb
WarningAveragestructurestendtobecrude.Minimizationisrecommended.
g_energy
Usethisprogramtoplotenergydata,pressure,volume,density,etc.
g_energyfmd.edrofws_pe.xvg 14
- 15. GROMACSTutorial
Youwillbepromptedforthespecificdatathatyouwanttoincludeintheoutputfile(*.xvg).The
outputfileisatypeofspreadsheetfilethatcanbereadusingXmgrorGrace.Thisfileisatextfile
andcanbereadintoMicrosoftExcelhowever,youwillneedtodosomelighteditingofthefile.
Forexampleinourcaseabove(yourresultsmaybedifferent),weseethefollowing
Selectthetermsyouwantfromthefollowinglist
G96AngleProperDih.ImproperDih.LJ14Coulomb14
LJ(SR)LJ(LR)Coulomb(SR)Coul.recip.Potential
KineticEn.TotalEnergyTemperaturePressure(bar)BoxX BoxYBoxZVolume
Density(SI)pV VirXXVirXYVirXZVirYXVirYY
VirYZVirZXVirZYVirZZPresXX(bar)
PresXY(bar)PresXZ(bar)PresYX(bar)PresYY(bar)PresYZ(bar)
PresZX(bar)PresZY(bar)PresZZ(bar)#Surf*SurfTenPcouplMuXX
PcouplMuYYPcouplMuZZMuXMuYMuZ TProteinTSOLTCL LambProteinLambSOL
LambCL Forpotential energy,typePotential Hitthekeyagain
WegetasummarywithaveragePEandRMSDinkJ/mol
Lastframeread500time100.000
Statisticsover50001steps[0.0000thru100.0000ps],1datasets Energy
AverageRMSDFluct.DriftTotDrift Potential
192661311.547311.5010.1846818.4684
Toread*.xvgfilesintoGraceusethefollowingcommand:
xmgracenxyfws_pe.xvg YoumayobtainGracefrom
http://plasmagate.weizmann.ac.il/Grace/.GracerunsonLinuxandin
Unixonly.
IfyoudonothaveGraceorXmgr,justimportorreadthe*.xvgfileintoMSExcelasa
spacedelimitedfile. g_gyrate
Useg_gyratetomeasuretheradiusofgyration.Thisquantitygivesameasureofthe
compactnessofthestructure.Thisgivesameasureofthemassoftheatom(s)relativethecenter
ofmassofthemolecule. g_gyratefmd.trrsmd.tpr ofws_gyrate.xvg
g_rmsandg_rmsdist 15
- 16. GROMACSTutorial
Theseprogramsareusefulformeasuringrootmeansquaredeviationsinthestructure.Useg_rms
toevaluatethedeviationofthestructurefromtheoriginalstartingstructureoverthecourseofthe
simulation.(Thedt10optiontellstheprogramtowriteeverytenthframe)
g_rmss*.tpr f *.xtc dt 10
TocomparermsdtotheNMRstructureusethefollowingcommand g_rmssem.tprf
md.trro fws_rmsd.xvg
Selectgroup4(Backbone)fortheleastsquaresfit.Theprogramwillgenerateaplotofrmsdover
time(rmsd.xvg)whichyoumayimportintoExcelasaspacedelimitedfile.
g_rmsf Computesrootmeansquarefluctuationofatompositions.Likeg_covar
thiscommandmaybe
usedtocomputeaveragestructures.Forexample,tocalculatetheaverageofthelast500psofa2
ns(2000ps)dynamicssimulation,usethefollowing g_rmsf f traj.xtcs
topol.tpr b1501 e2000 o traj_rmsf.xvgox traj_avg.pdb
SelectarangewhereyouobservesomeequilibriumfromyourRMSDplot(computedusing
g_rms).Forexample Theexampleaboveistheresultofa1nssimulation
(yourresultsmightbedifferent).This
simulationstillneedstoberunevenlongerasithasnotcompletelyequilibrated.
Intheexample above,wemightuse the200to500
psrangeforcomputinganaveragestructureasweobservea
levelingoffindeviationfromthereference(initialstructure).
Thecommandwouldbe g_rmsf smd.tprf md.trrb 200e 500ox fws_avg.pdb
16
- 17. GROMACSTutorial Selectgroup1Proteinwhenprompted.
WarningAveragestructurestendtobecrude.Minimizationisrecommended.
Suggestedem.mdpfilessetupforan
invacuominimization.Performsteepestdescentsfirst
followedbyconjugategradient. CAUTION!Youmayneedtorun pdb2gmx
tosetupanewsetof
topologyfilesforyourminimizationespeciallyifyouhaveisolatedaspecificgroupincomputing
youraveragestructure(asopposedtotheentiresystem).
SteepestDescentsinvacuo Userkerrigan(236) Inputfile
cpp=/usr/bin/cpp constraints=none integrator=steep nsteps=400
Energyminimizingstuff emtol=1000 emstep =0.01 nstcomm=1
ns_type=grid morse=no coulombtype=Shift vdw_type=Shift rlist=1.4
rcoulomb=1.2 rvdw=1.2 rcoulomb_switch= 1.0 rvdw_switch=1.0
epsilon_r=6.0 Tcoupl=no Pcoupl=no gen_vel=no
Conjugategradientwithmorsepotential invacuo Userkerrigan(236)
Inputfile cpp= /usr/bin/cpp constraints=none integrator=cg
nsteps=3000 Energyminimizingstuff emtol=100 emstep=0.01 17
- 18. GROMACSTutorial nstcgsteep=1000 nstcomm=1 morse= yes
coulombtype=Shift vdw_type=Shift ns_type=grid rlist=1.4
rcoulomb=1.2 rvdw=1.2 rcoulomb_switch=1.0 rvdw_switch=1.0
epsilon_r=6.0 Tcoupl=no Pcoupl=no gen_vel=no Theg_rmsf
commandmayalsobeusedtocomputetemperaturefactors.Thecomputed
temperaturefactorscanbecomparedtoxraycrystal structure
temperaturefactors. g_rmsf smd.tprf md.xtcormsf.xvgoqfws_bfac.pdb
UsetheBackbonegrouponceagain. 100 90 80 TemperatureFactor 70 60 50
40 30 20 10 0 0 50 100 150 200 250 300 Residue# do_dssp
Usethedo_dsspcommandtoanalyzethesecondarystructureofyourmodel.Youmusthavethe
dsspprogram
(http://swift.cmbi.ru.nl/gv/dssp/)installed(in/usr/local/bin).[9]
do_dsspsmd.tpr f md.xtcofws_ss.xpm
SelectGroup1(Protein)forthecalculation.Usethexpm2psprogram
toconvertthexpmfiletoeps
format.ThenusetheImageMagickconvertprogramtoconverttheepsfiletopngorwhatever
desiredimageformat. 18
- 19. GROMACSTutorial xpm2psffws_ss.xpm ofws_ss.eps
convertfws_ss.epsfws_ss.png
Whereresidue#isontheyaxisandtime(ps)isonthexaxis.Asseenfromtheoriginal
NMR structurebelow Fromthedsspplotabove,wesee3regionsof
redforthe3sheets(displayedinyellowinthe
structureimagetotheleft).Theoneshort
regioninthemiddleistheleaststable.The
imagetotheleftwaspreparedusingthePymol
program.(http://pymol.sourceforge.net/ ) g_hbond Useg_hbond
tomeasurethenumberofhydrogenbonds,hbonddistances&anglesbetween
moleculesorgroupsthroughthecourseofthesimulation. g_hbondf
md.trrsmd.tpr num fws_hnum.xvg H a r D A
Geometricalrelationsusedbyg_hbond. ThedefaultsinGromacs3.3.1are: r
0.35 nm a 30 19
- 20. GROMACSTutorial Usether
andaflagstosetotherlimits.Bydefault,g_hbondanalyzesthedonoracceptor(rDA)
distance).
Youmaychangethisbehaviourbysettingthedaflagtono.Settingdatonoinstructs
g_hbondtoanalyzetherHA distance. SeetheGromacsmanualformoreoptions.
g_saltbr Useg_saltbr
toanalyzesaltbridgesbetweenresiduesinyoursimulation.
Theprogramoutputsa
setof*.xvgfiles,whichgivedistancesbetweenminus/minus,chargedresiduesplus/minus(the
mostinteresting)andplus/pluschargedresidues. g_saltbr
fmd.trrsmd.tpr
HowToSavespecifictimepointsfromatrajectoryas*.PDBfiles:
Togetaspecificframe(3000psinthisexample)insteadofthewholetrajectoryasapdbfileuse
additionallythedumpoption,e.g. trjconvf traj.xtcsfile.tpro
time_3000ps.pdb dump3000 20
- 21. GROMACSTutorial
Performotheranalysistasksasrecommendedbyyourinstructor. Appendix.
Howtorestartacrashedrun. tpbconv sprev.tpr f prev.trr eprev.edro
restart.tpr mdrunsrestart.tpr deffnmmyrestart (thedeffnm
optionsetsthedefaultfilenameforallfile optionstomdrun)
Howtoextendarun. tpbconv f traj.trr s topol.tpr eener.edr o
tpxout.tpr time$VALUEuntil $VALUE
Where$VALUE=ps(e.g.ifyouwantedtoextenda2nsrunto5ns,then$VALUE=5000)
Howtosetupaparallelrun gromppnp#f md.mdpcpr.gropfws.topo md.tpr
Wherethenpflagisusedtodesignatethenumberofnodesforparallelexecution.
Thenusemdrun_mpitoruntheparalleljob.ForexampleontheUMDNJSunFireuse
mprunnp#/products/gromacs/sparcsunsolaris2.8/bin/mdrun_mpideffnmmd
UsetheabovecommandinyourSunGridEnginebatchsubmissionscript!
Bibliography 1.
Lindahl,E.,B.Hess,andD.vanderSpoel,GROMACS3.0:apackageformolecular
simulationandtrajectoryanalysis.J.Mol.Model,2001.7:p. 306317. 2.
Berendsen,H.J.,J.Grigera,andT.Straatsma,Themissingtermineffectivepairpotentials.
J.Phys.Chem.,1987.91:p.62696271. 3. Hess,B.andN.vanderVegt,
Hydrationthermodynamicpropertiesofaminoacid
analogues:asystematiccomparisonofbiomolecularforcefieldsandwatermodels.J.Phys.
Chem.B,2006.110(35):p.1761626. 4.
Weber,W.,P.H.Hnenberger,andJ.A.McCammon,MolecularDynamicsSimulationsofa
PolyalanineOctapeptideunderEwaldBoundaryConditions:InfluenceofArtificial
PeriodicityonPeptideConformation.J.Phys.Chem.B,2000.104(15):p.36683575.
5.
Darden,T.,D.York,andL.Pedersen,ParticleMeshEwald:AnNlog(N)methodforEwald
sumsinlargesystems.J.Chem.Phys.,1993.98:p.1008910092. 6.
Essmann,U.,L.Perera,M.L.Berkowitz,T.Darden,H.Lee,andL.Pedersen,Asmooth
particlemeshewaldpotential.J.Chem.Phys.,1995.103:p.85778592.
21
- 22. GROMACSTutorial 7.
Hess,B.,H.Bekker,H.Berendsen,andJ.Fraaije,LINCS:ALinearConstraintSolverfor
molecularsimulations.J.Comp.Chem.,1997.18:p.14631472. 8.
Berendsen,H.J.C.,J.P.M.Postma,W.F.vanGunsteren,A.DiNola,andJ.R.Haak,
Moleculardynamicswithcouplingtoanexternalbath.J.Chem.Phys.,1984.
81(8):p. 35843590. 9.
Kabsch,W.andC.Sander,Adictionaryofproteinsecondarystructure.Biopolymers,1983.
22:p.25772637. 22