Bhanu wrote:
Hi,
I'm using Gromacs 3.3.3, installed with double precision. When I run
genion with this command:
genion_d -s *.tpr -o *.gro -g genion.log -pot pot.pdb -p *.top -neutral
the following error message was generated:
------------------------------------------------------------------------
Program genion_d Version 3.3.3
sourcecode file: init.c, line 69
Fatal error:
run input file prakash.tpr was made for 32 nodes
while genion_d expected it to be for 1 node
------------------------------------------------------------------------------
System is "protein in water", dodecahedron box. Everything is fine till
energy minimisation. genion is failing.
Any clue??
The problem is that genion is not MPI code, i.e., not parallelized. Usually one
does all of the preparation steps (pdb2gmx, editconf, genion) at one time, then
begins MPI work - minimization, equilibration, production.
-Justin
Thanks.
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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