[gmx-users] mdrun (nvt.mdp) wouldn't work

[Justin Lemkul]

On 11/29/17 5:02 PM, MD wrote:
> Hi gromacs folks,
>
> I was trying to do a mdrun using nvt.mdp and I got following error
> messages. I am not quite sure what is causing the error and I am hoping to
> get some help here. Is it because my starting structure is not good enough?
> There were some broken residues but I had them fixed and the minimization
> run was ok until the equilibration.
>
> The command and notes  I had was as followed.
>
>
> *  gmx grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr*
>
> Ignoring obsolete mdp entry 'title'
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.12#
> Setting the LD random seed to 552293178
> Generated 97877 of the 97903 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 1
> Generated 64492 of the 97903 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
> turning all bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'Ion_chain_A2'
> turning all bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'Other_chain_B'
> turning all bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'Protein_chain_C'
> turning all bonds into constraints...
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning all bonds into constraints...
> Excluding 1 bonded neighbours molecule type 'NA'
> turning all bonds into constraints...
>
> NOTE 1 [file topol.top, line 53]:
>    System has non-zero total charge: 0.140005
>    Total charge should normally be an integer. See
>    http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>    for discussion on how close it should be to an integer.

This is the same error as your previous question. Don't ignore grompp 
when it's trying to help you avoid really bad mistakes.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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