[gmx-users] REMD problem
Liu, Liang
liu4gre at gmail.com
Wed Sep 28 22:19:22 CEST 2011
So if my personal computer have 2 cores, the np should be set to 2? Does it
relate to -multi?
How to choose a reasonable number for -replex? the smaller the better?
Thanks again.
On Wed, Sep 28, 2011 at 3:06 PM, Justin A. Lemkul <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>> 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>
>> >>
>> <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>
>> <tel:%28540%29%20231-9080>
>> 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>
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>> >
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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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