Roll-to-roll gravure (R2Rg) has become highly affiliated with printed electronics in the past few years due to its high yield of printed thin-film transistor (TFT) in active matrix devices, and to its low cost. For printing TFTs with multilayer structures, achieving a high-precision in overlay printing registration accuracy (OPRA) is a key challenge to attain the high degree of TFT integration through R2Rg. To address this challenge efficiently, a digital twin paradigm was first introduced in the R2Rg system with an aim to optimize the OPRA by developing a predictive model based on typical input variables such as web tension, nip force, and printing speed in the R2Rg system. In our introductory-level digital twin, errors in the OPRA were collected with the variable parameters of web tensions, nip forces, and printing speeds from several R2Rg printing processes. Subsequently, statistical features were extracted from the input data followed by the training of a deep learning long-short term memory (LSTM) model for predicting machine directional error (MD) in the OPRA. As a result of training the LSTM model in our digital twin, its attained accuracy of prediction was 77%. Based on this result, we studied the relationship between the nip forces and printing speeds to predict the MD error in the OPRA. The results indicated a correlation between the MD error in the OPRA and the printing speed, as the MD error amplitude in the OPRA tended to decline at the higher printing speed.