[gmx-users] lennard jones

[Justin Lemkul]

On 4/22/16 2:56 PM, Alexander Alexander wrote:
> 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
>

You need cutoff-scheme = group if you're using tabulated interactions.

-Justin

> 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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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================