[gmx-users] REMD problem

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 28 22:06:34 CEST 2011



Liu, Liang wrote:
> This works. Thanks a lot.
> 
> Currently I am running on an RNA molecule and I want to a 1 ns REMD 
> simulations with 50 temperatures,
> would you please have a look at the following command "mpirun -np 50 
> mdrun_mpi -s md.tpr -multi 50 -replex 50". Is this right?
> How to choose the numbers for np, multi or replex?
> 

Current Gromacs versions allow more than one processor per REMD simulation. 
Please refer to the link I provided before for specifics.  You need all of the 
replicas to run at roughly the same speed so the number of processors per 
simulation should be the same.

> Is the simulation time still set in the mdp file with nsteps and dt? 
> e.g. nsteps = 500000 and dt = 0.002 to run a 1ns simulation?
> 

It's just like any other simulation in this regard.

-Justin

> Any helps will be highly appreciated.
> 
> On Wed, Sep 28, 2011 at 1:27 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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>
>         <mailto: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>>
>                <mailto: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>>
>                        
>          <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>
>         <http://vt.edu> | (540)
> 
>                231-9080 <tel:%28540%29%20231-9080>
>                   <tel:%28540%29%20231-9080>
> 
>                  
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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> <http://vt.edu> | (540)
>         231-9080 <tel:%28540%29%20231-9080>
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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

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