Performance of the general amber force field in modeling aqueous POPC membrane bilayers.

@article{citeulike:1413339, abstract = {The aim of this work was to answer the question of whether the general amber force field (GAFF) is good enough to simulate fully hydrated POPC membrane bilayers. The test system contained 128 POPC and 2985 TIP3P water molecules. The equilibration was carried out in a nonarbitrary manner to reach the stable liquid-crystalline phase. The simulations were performed by using particle mesh Ewald electrostatics implemented in molecular dynamics packages Amber8 (NPT ensembles) and NAMD2 (NPgammaT ensembles). The computational results were assessed against the following experimental membrane properties: (i) area per lipid, (ii) area compressibility modulus, (iii) order parameter, (iv) gauche conformations per acyl chain, (v) lateral diffusion coefficients, (vi) electron density profile, and (vii) bound water at the lipid/water interface. The analyses revealed that the tested force field combination approximates the experimental values at an unexpectedly good level when the NPgammaT ensemble is applied with a surface tension of 60 mN m(-1) per bilayer. It is concluded that the GAFF/TIP3P combination can be utilized for aqueous membrane bilayer simulations, as it provides acceptable accuracy for biomolecular modeling. (c) 2007 Wiley Periodicals, Inc. J Comput Chem, 2007.}, address = {Department of Chemistry and Chemical Informatics, Faculty of Education, University of Szeged, Boldogasszony sgt. 6, H‐6725 Szeged, Hungary.}, author = {J\'{o}j\'{a}rt, Bal\'{a}zs and Martinek, Tam\'{a}s A A. }, citeulike-article-id = {1413339}, doi = {http://dx.doi.org/10.1002/jcc.20748}, issn = {0192-8651}, journal = {J Comput Chem}, keywords = {amber, dynamics, md, membrane, modeling, theory}, month = {April}, number = {12}, pages = {2051--2058}, posted-at = {2007-06-26 13:32:45}, priority = {2}, title = {Performance of the general amber force field in modeling aqueous POPC membrane bilayers.}, url = {http://dx.doi.org/10.1002/jcc.20748}, volume = {28}, year = {2007} }

TY - JOUR ID - citeulike:1413339 L3 - citeulike-article-id:1413339 TI - Performance of the general amber force field in modeling aqueous POPC membrane bilayers. JF - J Comput Chem VL - 28 IS - 12 SP - 2051 EP - 2058 AD - Department of Chemistry and Chemical Informatics, Faculty of Education, University of Szeged, Boldogasszony sgt. 6, H‐6725 Szeged, Hungary. SN - 0192-8651 N2 - The aim of this work was to answer the question of whether the general amber force field (GAFF) is good enough to simulate fully hydrated POPC membrane bilayers. The test system contained 128 POPC and 2985 TIP3P water molecules. The equilibration was carried out in a nonarbitrary manner to reach the stable liquid-crystalline phase. The simulations were performed by using particle mesh Ewald electrostatics implemented in molecular dynamics packages Amber8 (NPT ensembles) and NAMD2 (NPgammaT ensembles). The computational results were assessed against the following experimental membrane properties: (i) area per lipid, (ii) area compressibility modulus, (iii) order parameter, (iv) gauche conformations per acyl chain, (v) lateral diffusion coefficients, (vi) electron density profile, and (vii) bound water at the lipid/water interface. The analyses revealed that the tested force field combination approximates the experimental values at an unexpectedly good level when the NPgammaT ensemble is applied with a surface tension of 60 mN m(-1) per bilayer. It is concluded that the GAFF/TIP3P combination can be utilized for aqueous membrane bilayer simulations, as it provides acceptable accuracy for biomolecular modeling. (c) 2007 Wiley Periodicals, Inc. J Comput Chem, 2007. KW - amber KW - dynamics KW - md KW - membrane KW - modeling KW - theory AU - Jójárt, Balázs AU - Martinek, Tamás A PY - 2007/04/12/ UR - http://dx.doi.org/10.1002/jcc.20748 ER -