[gmx-users] REMD problem
Liu, Liang
liu4gre at gmail.com
Wed Sep 28 22:00:31 CEST 2011
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?
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?
Any helps will be highly appreciated.
On Wed, Sep 28, 2011 at 1:27 PM, Justin A. Lemkul <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>> 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>
>> >
>> <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://vt.edu/Pages/Personal/justin>
>> >
>>
>> <http://www.bevanlab.biochem._**_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://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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