[gmx-users] Error in the replica order in REMD (GMX v2016.1)

[Hermann, Johannes]

I solved it rather the brute force way: In the shell script which I 
execute to run all my simulations I defined a variable for my Multidir 
and filled it with all the directories (which were then in order).
somewhere in the shell script:

[...]

MULTIDIR=""
LAMBDALIST=(0 1 2 3 4 5)
$MDRUN=Your_Individua_MDrun_command
$FREE_ENERGY=YOUR_INDIVIDUAL_DIRECTORY

for i in ${LAMBDALIST[@]}; do
   LAMBDA=$i
   cd $FREE_ENERGY
   mkdir Lambda_$LAMBDA
   cd $FREE_ENERGY/Lambda_$LAMBDA
   mkdir Production_MD
   cd Production_MD
   MULTIDIR="$MULTIDIR $FREE_ENERGY/Lambda_$LAMBDA/Production_MD"
done

$MDRUN -v -deffnm fec -multidir $MULTIDIR -replex 1000

You can adapt this for your needs.

On 02.08.2017 13:11, Mark Abraham wrote:
> Hi,
>
> The shell expansion is sorted alphabetically, rather than numerically, so
> the order is md_0, md_1, md_10, md_11, etc. Either make your directories
> like md_000, md_001, md_002, so the sortings are the same, or use a more
> complex wildcard like -multidir md_[0-9] md_[1-9][0-9]
>
> Mark
>
> On Wed, Aug 2, 2017 at 1:06 PM ABEL Stephane <Stephane.ABEL at cea.fr> wrote:
>
>> Hello again
>>
>> Thanks to J. Hermann  I can start my simulations, however few seconds
>> after the beginning of the run I have the following error
>>
>> "Replicas with indices 2 < 12 have temperatures 271.9 > 254.27, please
>> order your replicas on increasing temperature"
>>
>> I do not understand this error, since my replicas seem well ordered (i
>> think) : ref_t in replicas 2 is 254.27 K  and ref_t in replicas 12 is
>> 271.9) I check this with the ref_t in the mdp. For this calculation I used
>> the cpt file to generate the tpr.
>>
>> Could you help me again ?
>>
>> Stéphane
>>
>>
>>
>> --------------------------------------------------------------------
>> Stéphane Abel, Ph.D.
>>
>> CEA Saclay DSV/ISVFJ/SB2SM
>> Institut de Biologie Intégrative de la Cellule (I2BC)
>> Bat 528, Office 138C
>> Gif-sur-Yvette, F-91191 FRANCE
>> Phone (portable) : +33 6 49 37 70 60 <+33%206%2049%2037%2070%2060>
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-- 
______________________________________
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

Email: j.hermann at lrz.tum.de
http://www.biovt.mw.tum.de/