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

[nazli kashani javid]

thanks,
that's very kind of you.

On Sun, Feb 15, 2015 at 6:01 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
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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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