[gmx-users] nvt error

[Justin Lemkul]

On 8/10/14, 5:38 AM, Prajisha Sujaya 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
>

This warning implies that your input settings are designed for version 4.6 or 
5.0, but you are using an older (pre-4.6) version.

>
>
> 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
>

Self-explanatory.  Your input file is not sensible, and grompp is telling you 
what the problem is.

> 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.
>

Typically systems are neutralized with counterions in this case.

-Justin

-- 
==================================================

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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