[gmx-users] error in grompp run

[Mark Abraham]

On 13/06/2012 5:59 PM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Hi,
> I want to do a MD simulation in vacuum.

So don't turn on implicit solvent.

>   So first I wanted to prepare the
> files for that with "grompp".
> But there I got the error that
> "With GBSA implicit solvent, rgbradii must be equal to rlist"
>
> But the 2 values are the same in my .mdp file. Can you please show me
> where the failure is?
>
>
> define          = -DPOSRES
> integrator          =  md
> emtol = 1000.0
> emstep         = 0.01
> nsteps              =  50000
> nstlist             =  1
> ns_type             =  simple
> rgbradii            = 0
> rlist               =  0
> coulombtype         =  cutoff
> vdwtype             =  cutoff

These are misspelled.

See manual 7.3.9 for how to simulate without cut-offs.

Mark

> rcoulomb            =  0
> rvdw                =  0
> pbc                 =  no
> epsilon_rf          =  0
>
> implicit_solvent    = GBSA
> gb_algorithm        = HCT
> gb_epsilon_solvent  = 78.3
>
> nstxout             = 1
> nstfout             = 1
> nstvout             = 1
> nstxtcout           = 1
> nstlog              = 1
>
>
>
> Thank you,
> Eva
>