[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>
>
>
> http://www.bevanlab.biochem.______vt.edu/Pages/Personal/justin
> <http://vt.edu/Pages/Personal/justin>
> <http://vt.edu/Pages/Personal/__justin
> <http://vt.edu/Pages/Personal/justin>>
>
>
> <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>>>
>
> ==============================______==========
> -- gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> <mailto:gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org> <mailto:gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>__>
>
>
>
> http://lists.gromacs.org/______mailman/listinfo/gmx-users
> <http://lists.gromacs.org/____mailman/listinfo/gmx-users>
> <http://lists.gromacs.org/____mailman/listinfo/gmx-users
> <http://lists.gromacs.org/__mailman/listinfo/gmx-users>>
>
> <http://lists.gromacs.org/____mailman/listinfo/gmx-users
> <http://lists.gromacs.org/__mailman/listinfo/gmx-users>
> <http://lists.gromacs.org/__mailman/listinfo/gmx-users
> <http://lists.gromacs.org/mailman/listinfo/gmx-users>>>
> Please search the archive at
>
> http://www.gromacs.org/______Support/Mailing_Lists/Search
> <http://www.gromacs.org/____Support/Mailing_Lists/Search>
> <http://www.gromacs.org/____Support/Mailing_Lists/Search
> <http://www.gromacs.org/__Support/Mailing_Lists/Search>>
>
> <http://www.gromacs.org/____Support/Mailing_Lists/Search
> <http://www.gromacs.org/__Support/Mailing_Lists/Search>
> <http://www.gromacs.org/__Support/Mailing_Lists/Search
> <http://www.gromacs.org/Support/Mailing_Lists/Search>>> before
> posting!
> Please don't post (un)subscribe requests to the list.
> Use the www
> interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at __gromacs.org
> <mailto:gmx-users-request at gromacs.org>>
> <mailto:gmx-users-request@
> <mailto:gmx-users-request@>__gr__omacs.org <http://gromacs.org>
> <mailto:gmx-users-request at __gromacs.org
> <mailto:gmx-users-request at gromacs.org>>>.
>
> Can't post? Read
> http://www.gromacs.org/______Support/Mailing_Lists
> <http://www.gromacs.org/____Support/Mailing_Lists>
> <http://www.gromacs.org/____Support/Mailing_Lists
> <http://www.gromacs.org/__Support/Mailing_Lists>>
> <http://www.gromacs.org/____Support/Mailing_Lists
> <http://www.gromacs.org/__Support/Mailing_Lists>
> <http://www.gromacs.org/__Support/Mailing_Lists
> <http://www.gromacs.org/Support/Mailing_Lists>>>
>
>
>
>
> -- 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>
> <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>>
>
> ==============================____==========
> -- gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> http://lists.gromacs.org/____mailman/listinfo/gmx-users
> <http://lists.gromacs.org/__mailman/listinfo/gmx-users>
> <http://lists.gromacs.org/__mailman/listinfo/gmx-users
> <http://lists.gromacs.org/mailman/listinfo/gmx-users>>
> Please search the archive at
> http://www.gromacs.org/____Support/Mailing_Lists/Search
> <http://www.gromacs.org/__Support/Mailing_Lists/Search>
> <http://www.gromacs.org/__Support/Mailing_Lists/Search
> <http://www.gromacs.org/Support/Mailing_Lists/Search>> before
> posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at __gromacs.org
> <mailto:gmx-users-request at gromacs.org>>.
> Can't post? Read
> http://www.gromacs.org/____Support/Mailing_Lists
> <http://www.gromacs.org/__Support/Mailing_Lists>
> <http://www.gromacs.org/__Support/Mailing_Lists
> <http://www.gromacs.org/Support/Mailing_Lists>>
>
>
>
>
> --
> 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>
>
> ==============================__==========
> --
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/__mailman/listinfo/gmx-users
> <http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at
> http://www.gromacs.org/__Support/Mailing_Lists/Search
> <http://www.gromacs.org/Support/Mailing_Lists/Search> before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
> <http://www.gromacs.org/Support/Mailing_Lists>
>
>
>
>
> --
> 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
========================================
More information about the gromacs.org_gmx-users
mailing list