Thanks for the advice I re-complied everything again with static libraries and the installation went fine. But while executing the following command I am again getting error :- <br><br><br>mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 500 -v <br>
<br><br>Fatal error:<br>The number of nodes (1) is not a multiple of the number of simulations (3)<br>For more information and tips for troubleshooting, please check the GROMACS<br>website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>
-------------------------------------------------------<br><br>"BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff)<br><br>Halting program mdrun_mpi<br><br>gcq#155: "BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff)<br>
<br>application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0<br><br><br>I am trying to simulate 5 replicas and I have 4 cpu . <br><br><br><br><div class="gmail_quote">On Thu, Jan 12, 2012 at 1:37 PM, lina <span dir="ltr"><<a href="mailto:lina.lastname@gmail.com">lina.lastname@gmail.com</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">On Thursday 12,January,2012 08:54 AM, bharat gupta wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
I am trying to run a REMD of a peptide. But while executing the<br>
following command after nvt and npt equilibration , I am getting the<br>
following error:-<br>
<br>
mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000<br>
mdrun_mpi: error while loading shared libraries: libgmx_mpi.so.6: cannot<br>
enable executable stack as shared object requires: Permission denied<br>
</blockquote>
<br></div>
Can you run a normal md smoothly?<br>
try:<br>
mdrun_mpi mdrun -deffnm prefix_0<br>
<br>
if it works, then some of your trajectories not sound. means system does not equilibrium well.<div class="im HOEnZb"><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
Can anybody suggest me how could I rectify this error.<br>
<br>
--<br>
Bharat<br>
<br>
</blockquote>
<br></div><div class="HOEnZb"><div class="h5">
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Bharat<br>Ph.D. Candidate<br>Room No. : 7202A, 2nd Floor<br>Biomolecular Engineering Laboratory<br>Division of Chemical Engineering and Polymer Science<br>Pusan National University<br>
Busan -609735<br>South Korea<br>Lab phone no. - +82-51-510-3680, +82-51-583-8343<div>Mobile no. - 010-5818-3680<br>E-mail : <a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a></div><br>