[gmx-users] REMD problem
Justin A. Lemkul
jalemkul at vt.edu
Wed Sep 28 22:21:38 CEST 2011
Liu, Liang wrote:
> So if my personal computer have 2 cores, the np should be set to 2? Does
> it relate to -multi?
>
That means you can only run 2 replicates. Bad idea. You'll need access to a
much better cluster to do anything meaningful. All REMD simulations have to be
run simultaneously. If you want 50 replicas, you need at least 50 processors,
ideally more.
> How to choose a reasonable number for -replex? the smaller the better?
>
Please consult the literature.
-Justin
> Thanks again.
>
> On Wed, Sep 28, 2011 at 3:06 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> 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>
> <mailto: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>>
> <mailto: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>>>
> <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 <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>>>
>
> <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>
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> -- Best,
> Liang Liu
>
>
> -- ==============================______==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
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> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu>
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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)
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> Liang Liu
>
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> --
> ==============================__==========
>
> 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
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--
========================================
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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