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

[Justin Lemkul]

On 2/15/15 9:29 AM, nazli kashani javid wrote:
> thank you
>
> so I have to run different times !?
>

For any given simulation, you just use mdrun -rerun as many times as needed, 
with whatever groups are of interest.  Interaction energies are just 
post-processing measures, really.  They can be specified during the run or after 
the fact.

-Justin

> 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
>>>>
>>>> ==================================================
>>>> --
>>>> Gromacs Users mailing list
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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
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/
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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

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