[gmx-users] error using pme option

Chetan Mahajan chetanvm10 at gmail.com
Fri Jan 10 03:21:12 CET 2014

Hi Everyone,

I am new to Gromacs and currently facing following error when I use pme
coulombtype in my energy minimization run.

Reading file lnanop.tpr, VERSION 4.6.5 (single precision)
Using 4 MPI processes

Non-default thread affinity set probably by the OpenMP library,
disabling internal thread affinity
*mdrun_mpi: symbol lookup error:
/home/cmahajan/program/gmx_intel64/bin/../lib/libmd_mpi.so.8: undefined
symbol: DftiCreateDescriptor_s_1d*
(same for other MPI processes)

Is it that "pme" coulombtype requires libraries which are not in the path?
Please advise how to go forward.

Files (mdp and run) that I use are as follows.

1. mdp file:

;It gave message earlier wthen following was not commented out. Message was
"ignoring obselete mdp entry 'title' "
;title = Energy minimization of ligand_nanop-anatase-tio2

; Define can be used to control processes
define = -DFlEXIBLE

; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 10.0
nsteps = 500 ; Maximum number of (minimization) steps to perform
nstenergy = 1 ; Write energies to disk every nstenergy steps
energygrps = System ; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
ns_type = grid ; Method to determine neighbor list (simple, grid)
*coulombtype = pme ; Treatment of long range electrostatic interactions*
rcoulomb = 1.0 ; long range electrostatic cut-off
rvdw = 1.0 ; long range Van der Waals cut-off
constraints = none ; Bond types to replace by constraints
pbc = xyz ; Periodic Boundary Conditions (yes/no)

2. run file:

#PBS -S /bin/bash
#PBS -l nodes=1:ppn=4
#PBS -N energy_min3_18



# Set some environment variables
export PATH=/home/cmahajan/program/gmx_intel64/bin:$PATH

cd $begin3

#Energy minimization

mkdir 3_18
cd 3_18

mkdir min
cd min

grompp_mpi -f $begin3/min_lnanop3_18.mdp -c $begin3/lnanop.gro -p
$begin3/lnanop3_7.top -o lnanop.tpr

../../../../../../usr/local/bin/mpiexec -n 4  mdrun_mpi -deffnm lnanop


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