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

2017-01-13 Thread Kutzner, Carsten
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 below

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

2017-01-12 Thread qasimpars
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

2017-01-12 Thread Kutzner, Carsten
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 warning error > with those

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

2017-01-11 Thread Qasim Pars
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 equilibr

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

2017-01-11 Thread Kutzner, Carsten
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 constr

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

2017-01-10 Thread Qasim Pars
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 s