[gmx-users] REMD problem

[Justin A. Lemkul]

Liu, Liang wrote:
> 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?
> 

You have to run mdrun_mpi as a process under mpirun, e.g.:

mpirun -np 10 mdrun_mpi -s md.tpr (etc)

-Justin

> On Wed, Sep 28, 2011 at 1:02 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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>
>         <mailto: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> <http://vt.edu> | (540)
>         231-9080 <tel:%28540%29%20231-9080>
>            <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 <http://vt.edu> | (540) 231-9080
>     <tel:%28540%29%20231-9080>
>     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

-- 
========================================

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

========================================