From: Ole Juul Andersen (oja_at_chem.au.dk)
Date: Tue Jul 02 2013 - 12:33:45 CDT
Dear all,
We would like to run implicit solvent simulations of a protein complex (9135 atoms) using the GBIS model implemented in NAMD. However, we experience that the simulations are VERY slow. We have therefore been searching for errors in the configuration file and in the submit script, using the mailing list archive, the NAMD tutorial, and the NAMD user guide as resources. As none of these sources gave a helpful answer (we might have missed it?), we turned to the example files provided with the implicit solvent tutorial. The pdb file of ubiquitin contains 1231 atoms, and if we start a production run of 500 ns on a node with 12 cores (using the tutorial conf file), the simulation is estimated to take 1,000 hours. If we simply switch GBIS from 'on' to 'off' in the conf file, the time drops to ~200 hours. For both of these simulations, we see the time to expected completion rise (the GBIS 'on' simulation currently has 3500 hours remaining). This is the exact same problem that we experienced while running GBIS simulations on our own system. At one point, the log file stated that the job had over 10,000 hours remaining for less than 500 ns of simulation time and running on 4 nodes!
The jobs are run using NAMD2.8, however, the problem also occurs when they are run using NAMD2.9 on GPUs. The structures seem rather stable throughout the simulations, and I do therefore not believe that the increase in time to completion arises from an increase in neighbouring atoms (supported by the fact the the GBIS 'off' simulations also show an increase in simulation time). We don't experience problems when using explicit solvation and PME, as the time to completion decreases at a steady rate for these simulations. Have any of you experienced similar problems, and if so, did you manage to find the reason, or even better, the solution? The submit script and configuration file is presented below.
Thank you.
All the best,
Ole
------------------------------------- SUBMIT SCRIPT -------------------------------------
#!/bin/sh
# Request resources - ppn is the number of processors requested per node
#PBS -q q12
#PBS -l nodes=1:ppn=12
#PBS -l walltime=24:00:00
#PBS -m abe
#PBS -N ubq_test
# Find additional options on
# http://www.clusterresources.com/wiki/doku.php?id=torque:2.1_job_submission
# and try "man qsub"
#Directory where input files are to be found
export JOB=/home/oja/GPU/namd-tutorial-files/1-4-gbis/grendel
#SCR is where the job is run (could be redundant)
export SCR=/scratch/$PBS_JOBID
#The programdirectory
export PROG=/com/namd/NAMD_2.8_Linux-x86_64-OpenMPI
#Copy all(!) the input files to the scratch directory
export name=ubq
export confname=ubq_gbis_eq
cp -p $JOB/par_all27_prot_lipid.inp $SCR/
cp -p $JOB/$confname.conf $SCR/
cp -p $JOB/$name.psf $SCR/
cp -p $JOB/$name.pdb $SCR/
#Enter the working directory
cd $SCR
######################
# RUN THE SIMULATION #
######################
source /com/OpenMPI/1.4.5/intel/bin/openmpi.sh
mpirun -bynode --mca btl self,openib $PROG/namd2 +setcpuaffinity $confname.conf > "$confname"_1.log
rsync -rlptDz $SCR/* $JOB/
#That's it
----------------------------------------------------------------------------------------------
---------------------------------------- CONF FILE ----------------------------------------
#############################################################
## JOB DESCRIPTION ##
#############################################################
# Minimization and Equilibration of
# Ubiquitin in generalized Born implicit solvent
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure ubq.psf
coordinates ubq.pdb
set temperature 310
set outputname ubq_gbis_eq
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters par_all27_prot_lipid.inp
temperature $temperature
# Implicit Solvent
gbis on
alphaCutoff 12.0
ionConcentration 0.3
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 14.0
switching on
switchdist 13.0
pairlistdist 16.0
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Output
outputName $outputname
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 100
outputPressure 100
#############################################################
## EXTRA PARAMETERS ##
#############################################################
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 100
reinitvels $temperature
run 500000000 ;# 5ps
----------------------------------------------------------------------------------------------
Ph.D. student Ole J. Andersen
iNANO, University of Aarhus
Department of Chemistry, Aarhus University
Langelandsgade 140,
Building 1510-421
8000 Aarhus C
Denmark
Tel.: +45 87 15 53 16 / +45 26 39 61 50
Mail: oja_at_chem.au.dk<mailto:oja_at_chem.au.dk>
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