[gmx-users] Re: energy-mimisation-problem

[SANTU BISWAS]

On Sun, Nov 25, 2012 at 9:08 PM, SANTU BISWAS <santu.biswas85 at 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