[gmx-users] nvt error

[rama david]

Dear Prajisha,
     It seems that u dont have neutralized system.
paste your nvt.mdp file , as ur nvt file may have some problem  and
add -neutral command at the time of addition of ion ( genion ).
 And it will be better more if you paste your command so we can discuss
more.


With Best Wishes,
 Rama


On Sun, Aug 10, 2014 at 3:08 PM, Prajisha Sujaya <prajishasujaya at gmail.com>
wrote:

> *im running protein-ligand complex using GROMOS96 43a1 force field*
>
> *while performing nvt step im getting this error, i have used
> protein-ligand tutorial nvt file to run the complex*
>
> Ignoring obsolete mdp entry 'title'
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#
>
> WARNING 1 [file nvt.mdp, line 44]:
>   Unknown left-hand 'cutoff-scheme' in parameter file
>
>
>
> ERROR 1 [file nvt.mdp]:
>   With coulombtype = PME, rcoulomb must be equal to rlist
>   If you want optimal energy conservation or exact integration use
> PME-Switch
>
> Generated 279 of the 1225 non-bonded parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein'
> turning all bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'UNK'
> turning all bonds into constraints...
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning all bonds into constraints...
> Excluding 1 bonded neighbours molecule type 'CL'
> turning all bonds into constraints...
>
> NOTE 1 [file topol.top, line 22744]:
>   System has non-zero total charge: -9.999998
>   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.
>
>
>
> Setting gen_seed to 13237
> Velocities were taken from a Maxwell distribution at 300 K
>
> There was 1 note
>
> There was 1 warning
>
> -------------------------------------------------------
> Program grompp, VERSION 4.5.5
> Source code file: grompp.c, line: 1372
>
> Fatal error:
> There was 1 error in input file(s)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> "Every Sperm is Sacred" (Monty Python)
>
>  Please help me to rectify this error
> --
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