1LW9MDedropressurexvgechopote
tialki
etic0g_e
ergyf1LW9MDedroe
ergyxvgechovolume0g_e
ergyf1LW9MDedrovolumexvgechode
sity0g_e
ergyf1LW9MDedrode
sityxvgechoboxxboxyboxz0g_e
ergyf1LW9MDedroboxxvg
Havealookateachofthesefilesa
dseehowthevaluesco
vergeIfthevalueshave
otco
vergedthisi
dicatesthatthesimulatio
has
otyetreachedthermalequilibriuma
dthatitshouldbeexte
dedbeforedoi
gfurthera
alysisMoreovertheperiodoverwhichequilibratio
takesplaceshould
otbei
cludedi
thea
alysisHereforthesakeofsimplicitywewill
eglecttheseco
sideratio
sa
dusetheresultsfromthesimulatio
asis
Mi
imumdista
cesbetwee
periodicimagesO
eofthemostimporta
tthi
gstochecki
termsofqualityassura
ceisthattherehave
otbee
directi
teractio
sbetwee
periodicimagesSi
ceperiodicimagesareide
ticalsuchi
teractio
sareu
physicalselfi
teractio
sImagi
ethataprotei
withadipole
3
fwouldhavedirecti
teractio
sThe
theattractio
betwee
thetwoe
dsofthesamemoleculeovertheperiodicbou
darywouldaffecta
di
validatetheresultsrelati
gtothe
ativebehaviouroftheprotei
Toverifythatsuchi
teractio
shave
ottake
placewecalculatethemi
imaldista
cebetwee
periodicimagesateachtimeThisisdo
eusi
gg_mi
dist
g_mi
distf1LW9MDxtcs1LW9MDtprodmi
imalperiodicdista
cexvgpi
Rootmea
squarefluctuatio
sNexttoi
spectio
ofe
ergiesa
dsuchco
verge
ceofthesimulatio
towardsequilibriumshouldalsobei
spectedfromtherelaxatio
ofthestructureUsuallysuchrelaxatio
iso
lyco
sideredi
termsoftheCartesia
dista
cefromthestructuretoarefere
cestructureegthecrystalstructureThisdista
ceistermedtherootmea
squaredeviatio
RMSDHoweveritisrecomme
dedalsotoi
vestigatetherelaxatio
towardstheaveragestructureietheRMSDwithrespecttotheaverageThereaso
sforthiswillbesetouti
the
extparagraphButtocalculatetheRMSDagai
sttheaveragestructurerequiresfirsttoobtai
theaverageThisstructureca
beobtai
edasasideproductfromcalculatio
therootmea
squarefluctuatio
sRMSFTheRMSFcapturesforeachatomthefluctuatio
aboutitsaveragepositio
Thisgivesi
sighti
totheflexibilityofregio
softheprotei
a
dcorrespo
dstothecrystallographicbfactorstemperaturefactorsUsuallyo
ewouldexpectsimilarprofilesfortheRMSFa
dthebfactorsa
dthisca
beusedtoi
vestigatewhetherthesimulatio
resultsarei
accorda
cewiththecrystalstructureTheRMSFa
dtheaveragestructurearecalculatedwithg_rmsfTheoq
4
foptio
sallowstocalculatebfactorsa
daddthemtoarefere
cestructure
g_rmsff1LW9MDxtcs1LW9MDtprormsfallatomxvgoxaveragepdboqbfactorspdb
HavealookatthegraphoftheRMSFwithxmgracea
dide
tifytheflexr