sorry i attached a wrong file.
this is my inputs about the implcit solvent
integrator = md
dt = 0.005; ps !
nsteps = 2000 ; total 10 ns.
nstlog = 5000
nstxout = 0 ;1000
nstvout = 0 ;1000
Your EM is unrelated to dynamics. I mean, it could, but we don't know
anything about your simulated system. I am of course assuming that your
MPI setup is optimal for gmx and you actually get to use those 16
threads, assuming those aren't an emulation of some sort.
On 6/24/2018 1:33 AM,
Hi,
I have attached the energy minimization mdp file.
please look through it .
cpp =
/lib/cpp ; prepocessor of
the current machine
define =
-DFLEXIBLE ; -DPOSRES,
This input has no information about implicit solvent and a simple google
search immediately yields mdp examples using gbsa. As far as performance
is concerned, we don't know the specs of your machine or the size of
your system. With cutoff electrostatics and a cutoff of 5 nm, one can
expect
Hi,
I am trying to simulate a protein in an implicit solvent in groamcs using
amber ff99sb ildn .
the mdpfile that I am using is I have shown below:
integrator = md
dt = 0.001 ;0.005; ps !
nsteps = 500 ; total 5 ns.
nstlog =
