[gmx-users] error: Atom 1 in multiple Energy Mon. groups

[Justin Lemkul]

On 2/15/15 8:51 AM, nazli kashani javid wrote:
> Hi all
> I want to calculate interaction energy of my protein that includes 4
> individual chains(a,b,c and d). at first I define an index file. It
> contains:
> [ chaina ]
>   1    2    3    4 ...454
> [ chainb ]
> 455  456  457 ...919
> [ chainc ]
> 920  921  922 .... 1373
> [ chaind ]
> 1374 1375 1376 ....1838
> [ chainsab ]
>   1    2    3....919
> [ chainsac ]
>    1    2    3 ...454    920....1373
> [ chainsad ]
> ......
> [ chainsbc ]
> .....
> [ chainsbd ]
> ..........
> [ chainscd ]
> ........
> [ chainsabc]
> 1    2    3 .... 1373
> [ chainsacd ]
> 1    2    3 .....454   920 ...1838
> [ chainsabd ]
> ......
> [ chainsbcd ]
> ........
>
> I add these groups to .mdp file as following:
>
> energygrps  =  chaina chainb chainc  chaind chainsab  chainsac chainsad
> chainsbc chainsbd chainscd chainsabc chainsacd chainsabd chainsbcd
>
> when I use grompp command ( grompp -f md.mdp -c npt.gro -p topol.top -n
> chains.ndx -o mda.tpr)  , and face with this error :
>
> Fatal error:
> Atom 1 in multiple Energy Mon. groups (1 and 5)
> For more information and tips for troubleshooting, please check the GROMACS
>
>
> dose my index file need any modifications? is there any wrong with my mdp
> file?
> how could I solve my problem?
>

You can't have overlapping groups.  You'll have to do multiple energy 
evaluations to achieve what you want.

-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

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