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 <jalem...@vt.edu
<mailto:jalem...@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
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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>>
-Justin
-- ==============================____==========
Justin A. Lemkul
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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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<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>
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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 | (540) 231-9080
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