1) There are 2 main reasons why this can happen:
a) xtreg uses stronger assumptions which are violated, e.g. because some regressors are predetermined or endogenous. As a result, coefficient estimates could be closter to 0 with GMM and eventually insignificant.
b) Standard errors are generally much larger with GMM due to the possible weakness of the instruments. This raises the chance of getting statistically insignificant results.
2) Yes, and yes.
3) Yes, a full set of dummies generally leads to perfect collinearity.
4) If industry dummies are specified as instruments but they do not appear in that list, then the respective instruments are likely omitted due to some perfect collinearity. For difference GMM, this might be the case if those industry dummies are time-invariant.
5) Yes, the inclusion of L2.x1 as a regressor does not invalidate it as an instrument.
6) Yes, with nonlinear moment conditions a numerical optimization procedure is required, which can take much longer, especially when the data set is relatively large. The message "not concave" can be ignored if it only appears for intermediate iterations. If it appears for the final iteration, then there are numerical difficulties and the algorithm did not converge to a proper solution. In such a case, a simplification of the model is required, which usually involves fewer instruments or even the abandonment of nonlinear moment conditions.
7) This is similar in spirit to a difference GMM estimator, where X2 X3 are strictly exogenous and X1 is endogenous. People probably would not call it a "difference GMM" estimator because it does not exclusively use model(diff). Some people may even call it a "system GMM" estimator because it is based on a system of two models, model(mdev) and model(diff), but this could lead to confusion with the traditional system GMM estimator, which used model(diff) (or model(fod)) and model(level). There is no commonly accepted name for this kind of estimator.
8) No, xtdpdgmmfe uses a different syntax which some users might find easier. It then translates this syntax into the syntax required for xtdpdgmm. The computations are still performed with the latter command. Please see the help file for xtdpdgmmfe and my earlier post #450 in this Statalist topic. If needed, you can subsequently modify the xtdpdgmm command line displayed by xtdpdgmmfe.
9) Yes.
10) No, the Chudik-Pesaran estimator requires all variables to be either strictly exogenous or predetermined. xtdpdgmmfe "solves" this issue by switching to a specific version of a difference GMM estimator when endogenous variables are present.
11) Yes.
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