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
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
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
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
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
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
