[gmx-users] Atomistic Simulation

[Justin Lemkul]

On 12/4/13 9:50 AM, panzu wrote:
> The thing is when I tray to use the grompp comand:
>
> bash >> g_grompp  -f grompp.mdp -c tolu.pdb -p topol.top
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#
>
> NOTE 1 [file grompp.mdp]:
>    nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
>    nstcomm to nstcalcenergy
>
>
> -------------------------------------------------------
> Program g_grompp, VERSION 4.5.7
> Source code file: /builddir/build/BUILD/gromacs-4.5.7/src/kernel/topio.c,
> line: 656
>
> Fatal error:
> Syntax error - File tolu.itp, line 58
> Last line read:
> '[ moleculetype ]'
> Invalid order for directive moleculetype
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
>
> I do not why it crashes ... This is how my topol looks like
>
> #include "tolu.itp"
>

You need to define a parent force field before you can define molecules.  See 
Chapter 5 of the manual.

-Justin

> [ system ]
> Toluene
>
> [ molecules ]
>   _I0L 10
>
>
> --
> View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984p5013065.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>

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

Justin A. Lemkul, Ph.D.
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

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