RE: Minimization is taking a lot of computing time.

From: JC Gumbart (
Date: Wed Aug 10 2011 - 00:52:16 CDT

I think the minimization is hung, which happens sometimes. Try correcting errors in the initial structure and start again.

-----Original Message-----
From: [] On Behalf Of Norman Geist
Sent: Wednesday, August 10, 2011 12:45 AM
To: 'Kartheek'
Cc: Namd Mailing List
Subject: AW: namd-l: Minimization is taking a lot of computing time.


well timing says 0,48 s/step what sounds ok, maybe you will just have to wait. You should also know that namd doesn't converge and stop the minimization itself, it'll run till the supplied step count is reached. So in theory your simulation should took 19 minutes to finish. If it doesn't something is wrong. Have you compiled namd by yourself or is it a precompiled binary from the namd homepage. If self compiled, try the precompiled one maybe. Also you can set outputtiming little slower and look at the information which is printed then, maybe check if the timings are true. I have no explaination at the moment why your simulation tells half a second for one step but doesn't finish in hours. I also find that you have huge energys for vdw and pressure in comparision to bond and angle and also system size, maybe check this.

Mit freundlichen Grüßen

Norman Geist.

-----Ursprüngliche Nachricht-----
Von: [] Im Auftrag von Kartheek
Gesendet: Dienstag, 9. August 2011 13:07
Betreff: namd-l: Minimization is taking a lot of computing time.

Here i am providing an URL to access output file.
----- Original Message -----
From: "Kartheek" <>
Sent: Friday, August 5, 2011 3:23:42 PM
Subject: Minimization is taking a lot of computing time.

Dear NAMD users.
I am started running a minimization for a system of nearly 16,060 atoms,minimization has been running since 48 hours on an eight processor system. Here is my configuration file.Some one please tell me what is the reason behind such a long minimization process.
Thanks in advance.

# periodic boundary conditions

cellBasisVector1 122.0 0.0 0.0
cellBasisVector2 0.0 42.0 0.0
cellBasisVector3 0.0 0.0 40.0
cellOrigin 0.1 0.2 0.2
#extendedSystem md018_rst.xsc

xstfile min.xst
xstfreq 600 # same as dcd freq
wrapwater on # off is default
wrapall off # off is default

# simulation space partitioning

cutoff 10.0
switching on
switchdist 8.0
pairlistdist 12.0
#pairlistMinProcs 72
margin 4.0 # 0.0 is the default value

# timestep parameters

#numsteps 7200000
timestep 1.0 # in femtoseconds
firsttimestep 0
stepspercycle 24 # default

# basic dynamics
exclude scaled1-4
1-4scaling 1.0
temperature 300.0 # initial temperature (K)
dielectric 1.0 # default
rigidbonds none # options : none,water,all
rigidtolerance 1.0e-8
rigiditerations 100
usesettle on

# PME parameters
pme yes # 'on' is also possible
pmegridsizex 125
pmegridsizey 45
pmegridsizez 43
pmeinterporder 6

# Multiple timestep parameters
fullelectfrequency 6
nonbondedfreq 2
mtsalgorithm impulse
longsplitting c1
molly on
mollytolerance 0.00001
mollyiterations 100

# input files
coordinates ionized.pdb # PDB file
structure ionized.psf # Xplore PSF file
parameters par_all27_prot_na.inp # parameter file (CHARMM)
paratypecharmm on # (on or off) or (yes or no)
#binvelocities md018_rst.vel
#bincoordinates md018_rst.coor

# output files
outputname min_out
binaryoutput no
restartname min_rst
restartfreq 600
binaryrestart yes # default
dcdfile min_traj.dcd
dcdfreq 600
dcdunitcell no # 'yes' is default if periodic cell is used
veldcdfile min_traj.vel
veldcdfreq 600

# standard output
outputenergies 600
outputmomenta 600
outputpressure 600
outputtiming 600

# Temperature control
# Langevib dynamics parameters
#langevin on
#langevintemp 300.0
#langevindamping 5.0
#langevinpiston on # NVT(off), NPT(on)
#langevinpistontarget 1.0
#langevinpistonperiod 200.0
#langevinpistondecay 100.0
#langevinpistontemp 300.0

minimization on
numsteps 2400


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