Gdtyjr

I am attempting to use Minion Pro with the fontspec package in XeLaTeX, but am encountering problems with the vertical alignment of subscripts when used with certain Greek characters:

documentclass[a4paper,12pt,oldfontcommands]article
usepackageamsmath
usepackage[MnSymbol]mathspec
usepackageMnSymbol
defaultfontfeaturesLigatures=TeX
setallmainfontsMinion Pro

begindocument

beginequation
 V_textPSD = V_sV_msin(omega_r t + phi_!s)sinleft(omega_r t + phi_sright)
endequation

beginequation
 zeta_s varsigma_s gamma_s kappa_s phi_!s varphi_s theta_s xi_s Xi_s f_s p_s 6_6 6_p p_6
endequation

enddocument

As can be seen in the image, the subscripts for some letters are in the correct places, except for zeta, sigma variant, gamma, both phi variants, and lowercase xi.

There are many other answers around concerning the kerning of external fonts with XeLaTeX, but this doesn't seem to be the issue here as using a fix such as phi_!s only brings the subscripted character closer and does not change the vertical alignment (as I have put in two examples above).

Why is this occurring? Is it possible to prevent it?

Edit: See the last code for the suggested solution

Old answer:

Seems that typing the Greek letters by a Greek keyboard solves the problem.

After many tests, found that the next code works with my font:

documentclass[11pt,oneside]article

usepackageamsmath
usepackage[MnSymbol]mathspec
usepackageMnSymbol
defaultfontfeaturesLigatures=TeX
setallmainfontsLinux Libertine O
usepackagepolyglossia
setmainlanguagegreek
setotherlanguageenglish
setmainfontLinux Libertine O
%newfontfamilygreekfontLinux Libertine O

begindocument
selectlanguageenglish
beginequation
V_textPSD= V_sV_msin(omega_r t + φ_s)sinleft(omega_r t + φ_sright)
endequation

beginequationγ_s ζ_s ς_s κ_s φ_s varphi_s θ_s ξ_s Ξ_s f_s p_s 6_6 6_p p_6
endequation
beginequationgamma_s zeta_s varsigma_s kappa_s phi_s varphi_s theta_s xi_s Xi_s f_s p_s 6_6 6_p p_6
endequation
selectlanguagegreek
Κείμενο εδώ
enddocument

Try with your font too.

Output:

As you can see, the equation (2) where greek letters typed from a greek keyboard gives enough better results.

PS: You don't have to use greek as mainlanguage... You may remove it if not installed or something.

And without setallmainfontsLinux Libertine O
(with system default math fonts for greek -just for comparsion-)
I get:

Edit (suggested solution):

Many people want to use greek letters but they don't have a greek keyboard. But even they do have one, it is a bad practice (in my opinion) to write from the keyboard greek letters in your math. (Let's suppose you want to create a latex code from your xelatex or you want to translate in other language and don't want to change your math code too). Then the solution is to write with the usual way your math and just redefine the greek letters in your preamble as shown below:

documentclass[11pt,oneside]article 
usepackageamsmath
usepackage[MnSymbol]mathspec
usepackageMnSymbol
defaultfontfeaturesLigatures=TeX
setallmainfontsLinux Libertine O
usepackagepolyglossia
setmainlanguagegreek
setotherlanguageenglish
setmainfontLinux Libertine O
%newfontfamilygreekfontLinux Libertine O

% Definitions of Greek (in math mode)
defalphaα
defbetaβ
defgammaγ
defdeltaδ
defepsilonε
defzetaζ
defetaη
defthetaθ
defiotaι
defkappaκ
deflambdaλ
defmuμ
defnuν
defxiξ
%defοo
defpiπ
defrhoρ
defsigmaσ
deftauτ
defupsilonυ
defphiφ
defvarphiϕ
defchiχ
defpsiψ
defomegaω
defvarsigmaς
defvarrhoϱ
defvarthetaϑ

defAlphaΑ
defBetaΒ
defGammaΓ
defDeltaΔ
defEpsilonΕ
defZetaΖ
defEtaΗ
defThetaΘ
defIotaΙ
defKappaΚ
defLambdaΛ
defMuΜ
defNuΝ
defXiΞ
%defΟO
defPiΠ
defRhoΡ
defSigmaΣ
defTauΤ
defUpsilonΥ
defPhiΦ
defChiΧ
defPsiΨ
defOmegaΩ

begindocument
selectlanguageenglish

English text

[
alpha_α
beta_β
gamma_γ
delta_δ
epsilon_ε
zeta_ζ
eta_η
theta_θ
iota_ι
kappa_κ
lambda_λ
mu_μ
nu_ν
xi_ξ
%ο_o
pi_π
rho_ρ
sigma_σ
tau_τ
upsilon_υ
phi_φ
varphi_ϕ
chi_χ
psi_ψ
omega_ω
varsigma_ς
varrho_ϱ
vartheta_ϑ]
[
Alpha_Α
Beta_Β
Gamma_Γ
Delta_Δ
Epsilon_Ε
Zeta_Ζ
Eta_Η
Theta_Θ
Iota_Ι
Kappa_Κ
Lambda_Λ
Mu_Μ
Nu_Ν
Xi_Ξ
%Ο_O
Pi_Π
Rho_Ρ
Sigma_Σ
Tau_Τ
Upsilon_Υ
Phi_Φ
Chi_Χ
Psi_Ψ
Omega_Ω
]


selectlanguagegreek

Ελληνικό κείμενο εδώ
enddocument

Output: