discrete energy value after restart

From: Kang Hee Cho (gkdkang_at_gmail.com)
Date: Thu Jan 20 2011 - 21:25:46 CST

Hi, everyone.

I am trying to simulate a protein using NAMD, but I am having a
problem with discrete energy value.

I want to simulate protein with NAMD 3 steps.
First, minimization. (all atoms are fixed except backbone)
Second, minimization with the backbone of the protein fixed.
Third, execution with the backbone fixed.

I restarted my protein but I found that the energy of the last step of
the first minimization and the starting step of the second one is
different.

Last step of first minimization
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY MISC
       KINETIC TOTAL TEMP POTENTIAL
  TOTAL3 TEMPAVG
ENERGY: 1000 58.4236 481.1728 286.8849 4.8477 -2588.3444 -91.7916
0.0000 0.0000 0.0000 -1848.8071 0.0000 -1848.8071 -1848.8071 0.0000

Starting step of second simulation
ENERGY: 1000 237.1904 2565.7394 553.0368 0.6446 -4628.9693 6496.4700
0.0000 0.0000 0.0000 5224.1119 0.0000 5224.1119 5224.1119 0.0000

I have tried a lot of things, but I don't know what to do.
Any help would be appreciated.

Cho

The molecule “qsu.psf”, “qsu.pdb” were used in the simulation.
The file “qsu_nw_eq.conf” was written for the first step and the file
“qsu_nw_eq2.conf” was for the second step

Another question is why I have to minimize whenever fixed atoms change
their position?

------------------------------------------
"qsu_nw_eq.conf"

structure          qsu.psf
coordinates        qsu.pdb

set temperature    300
set outputname     qsu_nw_eq

firsttimestep      0

# Input
paraTypeCharmm     on
parameters          par_all22_prot.inp
temperature         $temperature

# Force-Field Parameters
exclude             scaled1-4
1-4scaling          1.0
cutoff              13.5
switching           on
switchdist          10.
pairlistdist        16.5

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

# Output
outputName          $outputname

restartfreq         500     ;# 500steps = every 1ps
dcdfreq             50
outputEnergies      100
outputPressure      100

# Fixed Atoms Constraint
fixedAtoms          on
fixedAtomsFile      qsu_nw_eq.ref ;# all atoms are fixed except backbone

fixedAtomsCol       B

# Minimization
minimize            1000

--------------------------------------
"qsu_nw_eq2.conf"

structure          qsu.psf
coordinates        qsu.pdb
bincoordinates     qsu_nw_eq.coor
binvelocities      qsu_nw_eq.vel
#extendedSystem

set outputname     qsu_nw_eq2
firsttimestep      1000

# Input
paraTypeCharmm     on
parameters          par_all22_prot.inp

# Force-Field Parameters
exclude             scaled1-4
1-4scaling          1.0
cutoff              13.5
switching           on
switchdist          10.
pairlistdist        16.5

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

# Output
outputName          $outputname
restartfreq         500     ;# 500steps = every 1ps
dcdfreq             50
outputEnergies      100
outputPressure      100

# Fixed Atoms Constraint
fixedAtoms          on
fixedAtomsFile      qsu_nw_eq2.ref ;# backbone of the protein fixed

fixedAtomsCol       B

# Minimization
minimize            1000
run 1000
---------------------------------------------

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