[gmx-users] REMD problem

[Liu, Liang]

Thanks for the information. I installed the mpi version with "sudo apt-get
install gromacs-openmpi" under Ubuntu.

Then run "mdrun_mpi -s md.tpr -replex 10 -multi 10"?  Another error appears,
"The number of nodes (1) is not a multiple of the number of simulations
(10)". What is this for?

On Wed, Sep 28, 2011 at 1:02 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Liu, Liang wrote:
>
>> Does that mean I have to use MPI? I got an error "mdrun -multi is not
>> supported with the thread library.Please compile GROMACS with MPI support"
>> after run "mdrun -s md.tpr -multi 10 -replex 10"
>>
>>
> Per the error message, yes.
>
> -Justin
>
>  On Wed, Sep 28, 2011 at 12:58 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    Liu, Liang wrote:
>>
>>        Hi everyone,
>>        I tried to use Gromacs to run REMD simulation.
>>        Firstly a set of (md#).mdp file are make and the grompp command
>>        can generate the same amount of (md#).tpr file.
>>        Assume # = 10,
>>        then I tried to run REMD as mdrun -s md.tpr -np 10 -replex 10.
>>
>>        However, a fetal error shows as "Need at least two replicas for
>>        replica exchange (option -multi)", what is this for? Thanks.
>>
>>
>>
>>    You have to use the -multi flag.  Otherwise all mdrun does is run
>>    md.tpr and try to do REMD with nothing.
>>
>>    http://www.gromacs.org/__**Documentation/How-tos/REMD#__**
>> Execution_Steps<http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps>
>>    <http://www.gromacs.org/**Documentation/How-tos/REMD#**Execution_Steps<http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps>
>> >
>>
>>    -Justin
>>
>>    --     ==============================**__==========
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>    <tel:%28540%29%20231-9080>
>>
>>    http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>    <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >
>>
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>>
>> --
>> Best,
>> Liang Liu
>>
>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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-- 
Best,
Liang Liu
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