Network


Latest external collaboration on country level. Dive into details by clicking on the dots.

Hotspot


Dive into the research topics where Saeed Izadi is active.

Publication


Featured researches published by Saeed Izadi.


Journal of Physical Chemistry Letters | 2014

Building Water Models: A Different Approach

Saeed Izadi; Ramu Anandakrishnan; Alexey V. Onufriev

Simplified classical water models are currently an indispensable component in practical atomistic simulations. Yet, despite several decades of intense research, these models are still far from perfect. Presented here is an alternative approach to constructing widely used point charge water models. In contrast to the conventional approach, we do not impose any geometry constraints on the model other than the symmetry. Instead, we optimize the distribution of point charges to best describe the “electrostatics” of the water molecule. The resulting “optimal” 3-charge, 4-point rigid water model (OPC) reproduces a comprehensive set of bulk properties significantly more accurately than commonly used rigid models: average error relative to experiment is 0.76%. Close agreement with experiment holds over a wide range of temperatures. The improvements in the proposed model extend beyond bulk properties: compared to common rigid models, predicted hydration free energies of small molecules using OPC are uniformly closer to experiment, with root-mean-square error <1 kcal/mol.


PLOS ONE | 2013

Point Charges Optimally Placed to Represent the Multipole Expansion of Charge Distributions

Ramu Anandakrishnan; Charles M. Baker; Saeed Izadi; Alexey V. Onufriev

We propose an approach for approximating electrostatic charge distributions with a small number of point charges to optimally represent the original charge distribution. By construction, the proposed optimal point charge approximation (OPCA) retains many of the useful properties of point multipole expansion, including the same far-field asymptotic behavior of the approximate potential. A general framework for numerically computing OPCA, for any given number of approximating charges, is described. We then derive a 2-charge practical point charge approximation, PPCA, which approximates the 2-charge OPCA via closed form analytical expressions, and test the PPCA on a set of charge distributions relevant to biomolecular modeling. We measure the accuracy of the new approximations as the RMS error in the electrostatic potential relative to that produced by the original charge distribution, at a distance the extent of the charge distribution–the mid-field. The error for the 2-charge PPCA is found to be on average 23% smaller than that of optimally placed point dipole approximation, and comparable to that of the point quadrupole approximation. The standard deviation in RMS error for the 2-charge PPCA is 53% lower than that of the optimal point dipole approximation, and comparable to that of the point quadrupole approximation. We also calculate the 3-charge OPCA for representing the gas phase quantum mechanical charge distribution of a water molecule. The electrostatic potential calculated by the 3-charge OPCA for water, in the mid-field (2.8 Å from the oxygen atom), is on average 33.3% more accurate than the potential due to the point multipole expansion up to the octupole order. Compared to a 3 point charge approximation in which the charges are placed on the atom centers, the 3-charge OPCA is seven times more accurate, by RMS error. The maximum error at the oxygen-Na distance (2.23 Å ) is half that of the point multipole expansion up to the octupole order.


Journal of Chemical Physics | 2016

Accuracy limit of rigid 3-point water models.

Saeed Izadi; Alexey V. Onufriev

Classical 3-point rigid water models are most widely used due to their computational efficiency. Recently, we introduced a new approach to constructing classical rigid water models [S. Izadi et al., J. Phys. Chem. Lett. 5, 3863 (2014)], which permits a virtually exhaustive search for globally optimal model parameters in the sub-space that is most relevant to the electrostatic properties of the water molecule in liquid phase. Here we apply the approach to develop a 3-point Optimal Point Charge (OPC3) water model. OPC3 is significantly more accurate than the commonly used water models of same class (TIP3P and SPCE) in reproducing a comprehensive set of liquid bulk properties, over a wide range of temperatures. Beyond bulk properties, we show that OPC3 predicts the intrinsic charge hydration asymmetry (CHA) of water - a characteristic dependence of hydration free energy on the sign of the solute charge - in very close agreement with experiment. Two other recent 3-point rigid water models, TIP3PFB and H2ODC, each developed by its own, completely different optimization method, approach the global accuracy optimum represented by OPC3 in both the parameter space and accuracy of bulk properties. Thus, we argue that an accuracy limit of practical 3-point rigid non-polarizable models has effectively been reached; remaining accuracy issues are discussed.


Journal of Chemical Theory and Computation | 2015

Protein-Ligand Electrostatic Binding Free Energies from Explicit and Implicit Solvation.

Saeed Izadi; Boris Aguilar; Alexey V. Onufriev


International Journal for Numerical Methods in Fluids | 2013

Bin size determination for the measurement of mean flow velocity in molecular dynamics simulations

S. M. H. Karimian; Saeed Izadi


International Journal for Numerical Methods in Fluids | 2011

A study on the measurement of mean velocity and its convergence in molecular dynamics simulations

S. M. H. Karimian; Saeed Izadi; A. Barati Farimani


Journal of Chemical Theory and Computation | 2016

Implicit Solvent Model for Million-Atom Atomistic Simulations: Insights into the Organization of 30-nm Chromatin Fiber

Saeed Izadi; Ramu Anandakrishnan; Alexey V. Onufriev


Frontiers of Physics in China | 2018

High-temperature dynamic behavior in bulk liquid water: A molecular dynamics simulation study using the OPC and TIP4P-Ew potentials

Andrea Gabrieli; Marco Sant; Saeed Izadi; Parviz Seifpanahi Shabane; Alexey V. Onufriev; Giuseppe Baldovino Suffritti


Journal of Chemical Information and Modeling | 2017

Grid-Based Surface Generalized Born Model for Calculation of Electrostatic Binding Free Energies

Negin Forouzesh; Saeed Izadi; Alexey V. Onufriev


Biophysical Journal | 2015

Insights from All-Atom Molecular Dynamics Simulations of 40 Nucleosome Chromatin Fiber

Ramu Anandakrishnan; Saeed Izadi; Alexey V. Onufriev

Collaboration


Dive into the Saeed Izadi's collaboration.

Top Co-Authors

Avatar
Top Co-Authors

Avatar
Top Co-Authors

Avatar
Top Co-Authors

Avatar
Top Co-Authors

Avatar
Top Co-Authors

Avatar
Top Co-Authors

Avatar
Researchain Logo
Decentralizing Knowledge