energy jump running a simulation after minimization

From: Eva Gonzalez Noya (
Date: Tue Feb 15 2011 - 17:23:07 CST


I am learning how to use NAMD and found that when running a MD
simulation after a minimization the total energy suffers a jump when
switching from the minimization to the simulation run (the conf file I
am using is copied at the end of this message).

The most surprising thing is that in the log file there are two lines
with the same step number (the last step of minimization and the first
on of the MD run) and the energies are different for those lines:

ENERGY: 10 9830.6905 6728.5509 1233.5493
56.2839 -306280.7690 33101.0201 1709.8377
0.0000 0.0000 -253620.8366 0.0000
-253620.8366 -253620.8366 0.0000 -4869.3857
-4869.1463 639048.6136 -4869.3857 -4869.1463

ENERGY: 10 1330.6813 1237.8926 1233.3710
56.2073 -277911.3863 32478.0121 1710.0486
0.0000 0.0000 -239865.1735 0.0000
-239865.1735 -239868.4111 0.0000 -2159.4309
-2095.4452 639048.6136 -2159.4309 -2095.4452

As I minimized previously the structure for 16,000 steps I would expect
it to be close to the minimum so that when I do the MD simulation, atoms
shouldn't move much and the energy should be similar to the one of the
last step of the minimization.

Also I wonder whether the line labeled as 10 in the simulation run
corresponds to the evaluation of the energy before starting the
simulation or it corresponds to the energy after the first Molecular
Dynamics step. If it is the energy before starting the MD simulation I
think that I should exactly match the last step of the minimization,
doesn't it?

I copied below the conf file I am using (I am restarting it from a
previous minimization run of 16000 steps, so that I expect to be close
to a local minimum).

I tried already using the velocity restart files instead of assigning
the temperature a very small value and does not fix the problem.

Anyone found a similar problem before? Why is this jump in energy

Than you very much in advance for you help


structure ./apo-tubz_wb_ionized.psf
coordinates ./apo-tubz_wb_ionized.pdb

set temperature 0.000000001
set outputname apo-tubz_wb_ionized_eq

if {1} {
set inputname apo-tubz_wb_ionized_eq
binCoordinates $inputname.restart.coor
#binVelocities $inputname.restart.vel ;# remove the "temperature"
entry if you use this!
extendedSystem $inputname.xsc

firsttimestep 0

# Input
paraTypeCharmm on
temperature $temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 13.5

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

wrapAll on

# PME (for full-system periodic electrostatics)
PME yes
PMEGridSpacing 1.0

# Output
outputName $outputname

restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 1
outputPressure 100

# bound the Calpha of TubZ to harmonic springs with strength 100kcal/mol/A

constraints on
consexp 2
consref apo_tubz_fixed.pdb
conskfile apo_tubz_fixed.pdb
conskcol O
constraintScaling 100.0

minimize 10
run 10

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