Re: [gmx-users] Hydrogens of ATB ligand show obvious vibration under all-bonds contraints?

Dear GMX-Users, The vibration of the hydrogens of methyl and methylene groups was the result of Trajectory Smoothing in VMD, not the problem of GROMACS's all-bond constraints. Sorry for this distracting question. Yu > -Original Messages- > From: "Du, Yu" > Sent Time: 2019-10-18 08:20

[gmx-users] Coarse-grained MD

Dear Gromacs Users, I have surfactant and triglyceride united atom models which I used to do MD simulations with Gromacs. Now I want to do coarse grained MD simulations for the same systems using Gromacs. Appreciate, if anyone can guide me to setup the coarse grained simulation. Thank you. -- Be

Re: [gmx-users] Question about default auto setting of mdrun -pin

On Fri, Oct 18, 2019 at 4:36 PM wrote: > On Thu, Oct 17, 2019 at 10:34:39AM +, Kutzner, Carsten wrote: > > > > is it intended that the thread-MPI version of mdrun 2018 does pin to its > core > > if started with -nt 1 -pin auto? > No, I don't think that's intended. > > I think I have a (par

[gmx-users] Question about default auto setting of mdrun -pin

On Thu, Oct 17, 2019 at 10:34:39AM +, Kutzner, Carsten wrote: > > is it intended that the thread-MPI version of mdrun 2018 does pin to its core > if started with -nt 1 -pin auto? I think I have a (partial) idea about what's happening. get_thread_affinity_layout() performs various checks to de

Re: [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation

Dear Jorden, Many thanks for your reply. I have mentioned the files below for you to have a look. Once again thanks for your time. NVT.mdp:title = Protein-ligand complex NVT equilibrationdefine = -DPOSRES -DPOSRES_LIG ; position restrain the protein and ligand; Run parametersintegrator = md ; leap-

[gmx-users] Fatal error: no domain decomposition

Hi! I am trying to run a simple MD simulation as usual, but with this system I have got the same error message: *Fatal error:There is no domain decomposition for 160 ranks that is compatible with thegiven box and a minimum cell size of 1.02425 nmChange the number of ranks or mdrun option -rco

Re: [gmx-users] shift in trajectory

Dear Justin, Yes, they form a clear phase separation. Well, I did not clearly understand your last suggestion. I do not need to have their COM coordinate, I need COM of 'A' stays in the middle of the box. On Thu, Oct 17, 2019 at 5:17 PM Justin Lemkul wrote: > > > On 10/17/19 8:04 AM, Amin Rouy