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

[nazli kashani javid]

Thank you very much.

what do you mean of " multiple energy evaluations " ?

do you mean I should change my .mdp file like this:

energygrps  =  chaina chainb chainc  chaind
is it ok?

if I want to calculate interaction energy between ac and bd chains, what
should I do?

could you help me with more details about .mdp and .ndx files?

On Sun, Feb 15, 2015 at 5:23 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
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