[gmx-users] lennard jones

[Alexander Alexander]

Hello Mark,

Here is the mssage:

  gmx grompp -f mini.mdp -c ni.gro -p topol.top -o mini.tpr

Ignoring obsolete mdp entry 'optimize_fft'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#

ERROR 1 [file mini.mdp]:
  With Verlet lists only cut-off and PME LJ interactions are supported


ERROR 2 [file mini.mdp]:
  With Verlet lists only cut-off, reaction-field, PME and Ewald
  electrostatics are supported

Setting the LD random seed to 4013928268
Generated 1 of the 1 non-bonded parameter combinations
Excluding 1 bonded neighbours molecule type 'Ni'
Removing all charge groups because cutoff-scheme=Verlet

-------------------------------------------------------
Program gmx grompp, VERSION 5.1.2
Source code file:
/home/reuter/gromacs-5.1.2/src/gromacs/gmxpreprocess/grompp.c, line: 1738

Fatal error:
There were 2 errors in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Cheers,
Alex


On Fri, Apr 22, 2016 at 8:39 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> What was the actual error message, please?
>
> Mark
>
> On Fri, 22 Apr 2016 19:51 Alexander Alexander <alexanderwien2k at gmail.com>
> wrote:
>
> > Dear GMXuserr,
> >
> > To use LJ (6-9) in my simulation, I followed the manual as below:
> >
> > In .top file:
> > nbfunc        comb-rule
> >   1                   1
> >
> > In .mdp file:
> > coulombtype =  user
> > vdWtype       =  user
> >
> > Also, I provided a table.xvg for LJ(6-9) in my working directory.
> >
> > Normally invoked the "gmx grompp -f mini.mdp -c case.gro -p topol.top -o
> > mini.tpr"
> >
> > But it ends with a fatal error stating that cut-off and PME ... , must be
> > used for coulombtype and vdWtype.
> >
> > Would you please let me know where I am doing mistakenly or missing to do
> > so?
> >
> > Cheers,
> > Alex
> > --
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