[gmx-users] Problem with freeze groups

Hi gromacs users again, I have a problem with freezing of the atoms in my simulations. I have prepared kaolinite surface and have tried to run NVT simulation (see attached mdp file) with frozen outer layers (BULK section in my index file). I run it with GPU. While in 2016.5 version everything

[gmx-users] Fwd: H2SO4 (H2PO4-) force field

Hi gromacs user, I have a favour to ask you. Does anybody have working model of sulfuric acid and/or H2PO4- (exactly these species with two OH groups)? I have tried to prepared one according to various articles: loukonen2010 - Enhancing effect of dimethylamine in sulfuric acid nucleation in the

[gmx-users] Thermostatting in non-equilibrium dynamics

Dear all, The question I have has been posted here by other user last year but with not satisfactory answer (if I have searched properly!), so I'd like to open this topic again. It concerns non-equilibrium dynamics and thermostating. For simulations of Poisseuille flow in explicit atomistic slabs

Re: [gmx-users] h-bonds by g_hbond and VMD and ptraj

hD > Postdoctoral Research Fellow > Fulford JRF, Somerville College > > Department of Chemistry > Physical & Theoretical Chemistry Laboratory > University of Oxford > South Parks Road > Oxford > OX1 3QZ > > > On 2 Oct 2015, at 16:39, Ondrej Kroutil <ok

[gmx-users] h-bonds by g_hbond and VMD and ptraj

??? Thank you very much and enjoy upcoming weekend. Ondrej Kroutil -- Ondřej Kroutil ,, Faculty of Health and Social Studies "))' University of South Bohemia OOO Jirovcova 24, Ceske Budejovice OOO The Czech Rep

[gmx-users] 3dc + GPU

Hi gromacs users and developers, I have troubles with simulations of the system with surface (slab geometry) using GPU and Verlet cut-off scheme. When I run this simulation on CPU everything goes right and ions dissolved in the water above the surface seems to behave normally. But when I switch to