[gmx-users] simulation a box of water

[Justin Lemkul]

On 4/2/16 12:58 PM, Saeed Nasiri wrote:
> Dear users
>
> I used the "define= -DFLEXIBL" option and the problem within the energy
>> minimization step has been solved. However, there is another problem in the
>> nvt equilibration step. please help me with this problem!
>>
>
> Thanks in advanced.
>
>
> * ~/Desktop/water_box $ gmx_mpi grompp -f nvt.mdp -c em.gro -p topol.top -o
> nvt.tpr -maxwarn 1*
>                    :-) GROMACS - gmx grompp, VERSION 5.1.2 (-:
>
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> Bjelkmar
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>    Gerrit Groenhof   Christoph Junghans   Anca Hamuraru    Vincent Hindriksen
>   Dimitrios Karkoulis    Peter Kasson        Jiri Kraus      Carsten
> Kutzner
>      Per Larsson      Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff
>     Erik Marklund      Teemu Murtola       Szilard Pall       Sander Pronk
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> GROMACS:      gmx grompp, VERSION 5.1.2
> Executable:   /usr/local/gromacs/bin/gmx_mpi
> Data prefix:  /usr/local/gromacs
> Command line:
>    gmx_mpi grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -maxwarn 1
>
> Ignoring obsolete mdp entry 'title'
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
> Setting the LD random seed to 3338597373
> Generated 330891 of the 330891 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 330891 of the 330891 1-4 parameter combinations
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning all bonds into constraints...
> Setting gen_seed to 3746256358
> Velocities were taken from a Maxwell distribution at 300 K
> Removing all charge groups because cutoff-scheme=Verlet
> Analysing residue names:
> There are:  1000      Water residues
>
> -------------------------------------------------------
> Program gmx grompp, VERSION 5.1.2
> Source code file:
> /home/nasiri/gromacs-5.1.2/src/gromacs/gmxpreprocess/readir.c, line: 2585
>
>
>
>
>
> *Fatal error:Group Protein referenced in the .mdp file was not found in the
> index file.Group names must match either [moleculetype] names or custom
> index groupnames, in which case you must supply an index file to the '-n'
> optionof grompp.*
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>

It's right here:

> tc-grps            = Protein Non-Protein    ; two coupling groups - more

If you have only a box of water, you don't have protein...

-Justin

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

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

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