Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 192, Issue 89

Hi, I use gromacs-2019.4. Sent from my iPhone > On 25 Apr 2020, at 6:54 am, gromacs.org_gmx-users-requ...@maillist.sys.kth.se > wrote: > > Send gromacs.org_gmx-users mailing list submissions to >gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World

[gmx-users] Triclinic box is too skewed

} Box[2]={ 0.0e+00, 0.0e+00, 1.06717e+01} Can not fix pbc. Any suggestions about this? Thanks Regards -- *Jun ZHOU* Postgraduate Student , Room 117, Building 36 Department of Civil Engineering, Monash University, Victoria 3800, Australia. -- Gromacs Users mailing

[gmx-users] Ways to calculate shear viscosity

ays he has a patch for this. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2016-October/009325.html. Can anyone show me how to do this? Thanks. -- *Jun ZHOU* Postgraduate Student , Room 117, Building 36 Department of Civil Engineering, Monash University, Victoria 3800,

[gmx-users] Triclinic box is too skewed

efore, any suggestions will be appreciated. Thanks Regards, -- *Jun ZHOU* Postgraduate Student , Room 117, Building 36 Department of Civil Engineering, Monash University, Victoria 3800, Australia. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing

[gmx-users] Viscosity of non-newtonian fluid

Hi all, Can I use GROMACS to simulate the viscosity of non-newtonian fluid, namely, small polymer in water solution. Since the system is not a homogenous system, I am not sure periodic perturbation method will be feasible for it. Regards, -- *Jun ZHOU* Postgraduate Student , Room 117, Building

[gmx-users] Problems with Non-equilibrium MD

my mdp file, can anyone give me some suggestions? Thanks. Regards, -- *Jun ZHOU* Postgraduate Student , Room 117, Building 36 Department of Civil Engineering, Monash University, Victoria 3800, Australia. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

[gmx-users] Fwd: Problems with Non-equilibrium MD

also attached my mdp file, can anyone give me some suggestions? Thanks. Regards -- *Jun ZHOU* Postgraduate Student , Room 117, Building 36 Department of Civil Engineering, Monash University, Victoria 3800, Australia. -- Gromacs Users mailing list * Please search the archive at http

[gmx-users] How to use gmx h2order when using four point water model

Hi all, I want to obtain the water dipole orientation at the interface using gmx h2order. It works well when I I use 3 point water model, like SPC/E. The manual says that the order of water should be O H H, but for 4 point water model, there is a vitual atom, and this command cannot output the