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Hi there,
thanks for that. It makes clear.
Regards
and
------------------------------------------------------------
Andrea Spitaleri PhD
Dulbecco Telethon Institute
Center of Genomics, BioInformatics and BioStatistics
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://sites.google.com/site/andreaspitaleri/
Tel: 0039-0226434348/5622/3497/4922
Fax: 0039-0226434153
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________________________________________
Da: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] per conto di
Mark Abraham [mark.abra...@anu.edu.au]
Inviato: giovedì 14 ottobre 2010 3.16
A: Discussion list for GROMACS users
Oggetto: Re: [gmx-users] remd with disre in gmx4.0.7
On 14/10/2010 12:09 PM, Justin A. Lemkul wrote:
>
>
> Spitaleri Andrea wrote:
>>
>> ------------------------------------------------------------------------
>> <http://www.sanraffaele.org/grazieate>
>> ------------------------------------------------------------------------
>>
>> ------------------------------------------------------------------------
>>
>>
>> Hi there,
>> this is a very old issue for me at lest and I still get error running
>> a remd simulation using restraints for ion. I am using gmx4.0.7
>> This is my input:
>>
>> ; Distance restraints
>> disre = simple
>> disre_weighting = equal
>> disre_fc = 1000
>>
>> and in topol.top
>>
>> [ distance_restraints ]
>> ; ai aj type index type' low up1 up2 fac
>> 957 309 1 0 1 0.18 0.20 0.25 1
>> 957 338 1 1 1 0.18 0.20 0.25 1
>> 957 701 1 2 1 0.18 0.20 0.25 1
>> 957 733 1 3 1 0.18 0.20 0.25 1
>> 956 149 1 4 1 0.18 0.20 0.25 1
>> 956 185 1 5 1 0.18 0.20 0.25 1
>> 956 417 1 6 1 0.18 0.20 0.25 1
>> 956 462 1 7 1 0.18 0.20 0.25 1
>>
>> So all different restraints. My input run is:
>>
>> #PBS -l nodes=120
>> mpirun mdrun_d -s remd -v -deffnm remd -multi 5 -replex 5000 -npme 8
>> -dd 4 4 1
>>
>> and immediately I get:
>>
>> Program mdrun_d, VERSION 4.0.7
>> Source code file: disre.c, line: 143
>>
>> Fatal error:
>> Time or ensemble averaged or multiple pair distance restraints do not
>> work (yet) with domain decomposition, use particle decomposition
>> (mdrun option -pd)
>>
>> That's strange since I am not neither using time nor ensemble
>> averages nor multiple dist restraints.
>
> You are using ensemble averaging, which is invoked when combining
> "disre = simple" and mdrun -multi, per the manual. You should be able
> to use mdrun -pd, as the error message suggests.
That is, "disre = simple" and mdrun -multi combine to implement ensemble
averaging. This seems not to be what the OP wanted, which seemed to be
distance restraints with REMD. Other than using PD, there's no
work-around in 4.0.x or current code.
Mark
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