[gmx-users] error: Atom 1 in multiple Energy Mon. groups
nazli kashani javid
nazlikjavid at gmail.com
Sun Feb 15 15:13:03 CET 2015
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
>> [ 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
>> dose my index file need any modifications? is there any wrong with my mdp
>> 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 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
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