Re: [gmx-users] domain decomposition error in the energy minimization step

Hi Qasim, > On 12 Jan 2017, at 20:22, qasimp...@gmail.com wrote: > > Hi Carsten, > > I think I couldn't clearly explain the protocol that I follow. Sorry for > that. Firstly, I do the EM, nvt (100 ps), npt (100 ps) and md (100 ns) steps > for the equilibrium. In all those steps I use the

Re: [gmx-users] domain decomposition error in the energy minimization step

Hi Carsten, I think I couldn't clearly explain the protocol that I follow. Sorry for that. Firstly, I do the EM, nvt (100 ps), npt (100 ps) and md (100 ns) steps for the equilibrium. In all those steps I use the below free energy parameters for the forward state: free-energy = yes init-lambda

Re: [gmx-users] domain decomposition error in the energy minimization step

Hi Qasim, > On 11 Jan 2017, at 20:29, Qasim Pars wrote: > > Dear Carsten, > > Thanks. The forward state simulations works properly with mdrun -ntmpi 8 > -ntomp 2 or mdrun -ntmpi 4 -ntomp 4 as you suggested. > For the backward state GROMACS still gives too many lincs

Re: [gmx-users] domain decomposition error in the energy minimization step

Dear Carsten, Thanks. The forward state simulations works properly with mdrun -ntmpi 8 -ntomp 2 or mdrun -ntmpi 4 -ntomp 4 as you suggested. For the backward state GROMACS still gives too many lincs warning error with those mdrun commands in the md step, indicating the system is far from

Re: [gmx-users] domain decomposition error in the energy minimization step

Dear Qasim, those kinds of domain decomposition 'errors' can happen when you try to distibute an MD system among too many MPI ranks. There is a minimum cell length for each domain decomposition cell in each dimension, which depends on the chosen cutoff radii and possibly other inter-atomic

[gmx-users] domain decomposition error in the energy minimization step

Dear users, I am trying to simulate a protein-ligand system including ~2 atoms with waters using GROMACS-2016.1. The protocol I tried is forward state for the free energy calculation. The best ligand pose used in the simulations was got by AutoDock. At the beginning of the simulation GROMACS