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

[nazli kashani javid]

thank you

so I have to run different times !?

On Sun, Feb 15, 2015 at 5:46 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/15/15 9:12 AM, nazli kashani javid wrote:
>
>> 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?
>>
>>
> This will give you nonbonded energy decomposition of:
> A-B
> A-C
> A-D
> B-C
> B-D
> C-D
>
> e.g. all possible (non-redundant) combinations of individual chains.
>
>  if I want to calculate interaction energy between ac and bd chains, what
>> should I do?
>>
>>
> Then you need groups that are chains AC and chains BD in two groups.
>
> -Justin
>
>
>  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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> --
> ==================================================
>
> 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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> Gromacs Users mailing list
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