On Sun, Nov 25, 2012 at 9:08 PM, SANTU BISWAS <santu.biswa...@gmail.com> wrote:
> dear users,
>
> When performing a energy minimization of a
> polypeptide(formed by lysine-5-residues) in vacuum box by using
> Steepest Descent and also Conjugate Gradient methods in gromacs double
> precision,i noted that GROMACS never converges to emtol values under
> about 0.00001 kj/mol/nm.I have used the .mdp file which is given below
>
>
>
> title =
> cpp = /lib/cpp
> ;include =-I../top/
> define = -DFLEXIBLE
>
> ; RUN CONTROL PARAMETERS =
> integrator = steep
> ; start time and timestep in ps =
> tinit = 0
> dt = 0.001
> nsteps = 1000
> rlist = 0.9
> rcoulomb = 0.9
> ; Method for doing Van der Waals
> vdw-type = Cut-off
> ; cut-off lengths
> rvdw_switch = 0
> rvdw = 0.9
> ; Neighbour searching
> nstlist = 1
> ; ENERGY MINIMIZATION OPTIONS =
> emtol = 0.00001
> emstep = 0.1
> nstcgsteep = 1000
>
>
>
>
> santu
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