[gmx-users] Grompp error while using dual topology for free energy

[Justin Lemkul]

On Thu, Nov 21, 2013 at 4:27 PM, bipin singh <bipinelmat at gmail.com> wrote:

> Hi all,
>
> For calculating the free energy of solvation, I have defined the end states
> in the topology file.  But while executing grompp, it displays the error:
>
> Program grompp_mpi, VERSION 4.6.3
> Source code file: /sw/source/sandbox/gromacs-4.6.3/src/kernel/grompp.c,
> line: 518
>
> Fatal error:
> No molecules were defined in the system
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
>
> *mdp settings for free energy:*
>
> free-energy              = yes
> sc-alpha                 = 0
> sc-power                 = 1
> sc-r-power               = 6
> init-lambda-state        = 0
> fep-lambdas              = 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
> coul-lambdas             = 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
> nstdhdl                  = 100
> dhdl-print-energy        = yes
>
>
You forgot the couple-moltype keyword, so grompp has no idea what you're
transforming.

-Justin

-- 

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

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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