Re: [gmx-users] Dipole moment and dielectric constant - gmx dipoles

Dear Iman, your approach sounds reasonable. Have you checked that all your molecules are whole? In the trajectory all atoms are located inside your simulation box. This means that some molecules are split which will lead to huge dipole moments. Best Philip Sent from my phone, forgive brevity

[gmx-users] Rigid four atom molecule using LINCS

Dear all, Is there any way (possibly by use of virtual sites) to create a completely rigid molecule consisting of four atoms arranged in tetrahedral shape and simulate it using the LINCS constraints algorithm? Specifically we try to rebuild our H3O+ molecule below in a way that allows us to

Re: [gmx-users] a problem about ewald geometry=3dc

and the other surface is free and sometimes > some of water molecules (small number) escape from it. So is 3dc option > still applicable or I should return to original 3d method? > I appreciate your valuable suggestions. > Thanks > > Ali > > > On Tue, Jun 20, 2017 at 6:50 PM, Phil

Re: [gmx-users] a problem about ewald geometry=3dc

in the whole box! The whole technique is explained in this paper: http://dx.doi.org/10.1063/1.479595 Best Philip — Philip Loche Department of Physics Freie Universität Berlin Arnimallee 14, Room 0.3.30 14195 Berlin, Germany phone: +49 (0)30/838-55279 > On 19. Jun 2017, at 21:37, Ali Shom

Re: [gmx-users] Calculation of dielectric constant

. If its spherical take a look at the following paper: http://link.aps.org/doi/10.1103/PhysRevE.92.032718 <http://link.aps.org/doi/10.1103/PhysRevE.92.032718> Best Philip — Philip Loche Department of Physics Freie Universität Berlin Arnimallee 14, Room 0.3.30 14195 Berlin, Germany phone: +49