<font color="#000099"><font face="verdana,sans-serif">This works. Thanks a lot.</font></font><div><font color="#000099"><font face="verdana,sans-serif"><br></font></font></div><div><font color="#000099"><font face="verdana,sans-serif">Currently I am running on an RNA molecule and I want to a 1 ns REMD simulations with 50 temperatures,</font></font></div>
<div><font color="#000099"><font face="verdana,sans-serif">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?</font></font></div><div><font color="#000099"><font face="verdana,sans-serif">How to choose the numbers for np, multi or replex?</font></font></div>
<div><font color="#000099"><font face="verdana,sans-serif"><br></font></font></div><div><font color="#000099"><font face="verdana,sans-serif">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?</font></font></div>
<div><font color="#000099"><font face="verdana,sans-serif"><br></font></font></div><div><font color="#000099"><font face="verdana,sans-serif">Any helps will be highly appreciated.<br></font></font><br><div class="gmail_quote">
On Wed, Sep 28, 2011 at 1:27 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im"><br>
<br>
Liu, Liang wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks for the information. I installed the mpi version with "sudo apt-get install gromacs-openmpi" under Ubuntu.<br>
<br>
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?<br>
<br>
</blockquote>
<br></div>
You have to run mdrun_mpi as a process under mpirun, e.g.:<br>
<br>
mpirun -np 10 mdrun_mpi -s md.tpr (etc)<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
On Wed, Sep 28, 2011 at 1:02 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Liu, Liang wrote:<br>
<br>
Does that mean I have to use MPI? I got an error "mdrun -multi<br>
is not supported with the thread library.Please compile GROMACS<br>
with MPI support" after run "mdrun -s md.tpr -multi 10 -replex 10"<br>
<br>
<br>
Per the error message, yes.<br>
<br>
-Justin<br>
<br>
On Wed, Sep 28, 2011 at 12:58 PM, Justin A. Lemkul<br>
<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br></div><div><div></div><div class="h5">
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>> wrote:<br>
<br>
<br>
<br>
Liu, Liang wrote:<br>
<br>
Hi everyone,<br>
I tried to use Gromacs to run REMD simulation.<br>
Firstly a set of (md#).mdp file are make and the grompp<br>
command<br>
can generate the same amount of (md#).tpr file.<br>
Assume # = 10,<br>
then I tried to run REMD as mdrun -s md.tpr -np 10<br>
-replex 10.<br>
<br>
However, a fetal error shows as "Need at least two<br>
replicas for<br>
replica exchange (option -multi)", what is this for? Thanks.<br>
<br>
<br>
<br>
You have to use the -multi flag. Otherwise all mdrun does is run<br>
md.tpr and try to do REMD with nothing.<br>
<br>
<a href="http://www.gromacs.org/____Documentation/How-tos/REMD#____Execution_Steps" target="_blank">http://www.gromacs.org/____<u></u>Documentation/How-tos/REMD#___<u></u>_Execution_Steps</a><br>
<<a href="http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps" target="_blank">http://www.gromacs.org/__<u></u>Documentation/How-tos/REMD#__<u></u>Execution_Steps</a>><br>
<<a href="http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps" target="_blank">http://www.gromacs.org/__<u></u>Documentation/How-tos/REMD#__<u></u>Execution_Steps</a><br>
<<a href="http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps" target="_blank">http://www.gromacs.org/<u></u>Documentation/How-tos/REMD#<u></u>Execution_Steps</a>>><br>
<br>
-Justin<br>
<br>
-- ==============================<u></u>____==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
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-- Best,<br>
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<br>
<br>
-- ==============================<u></u>__==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
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Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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Best,<br>
Liang Liu<br>
</div></div></blockquote><div><div></div><div class="h5">
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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