Energy problem after restart

From: Alessandro Pedretti (alessandro.pedretti_at_unimi.it)
Date: Thu Nov 20 2003 - 07:13:56 CST

Hi all !
I restarted my simple dynamics but I found that the energy of the last step
of the first simulation and the starting step of the second one is
different.

Last step of the first dynamics:

TIMING: 860000 CPU: 354917, 0.589419/step Wall: 354917, 0.589419/step,
22.9218 hours remaining, 0 kB of memory in use.
ENERGY: 860000 3709.6508 5116.2602 2992.5010
6.9421 -21150.7474 -9771.7463 0.2589 0.0000
12444.9404 -6491.9403 144.6908 -6383.8469 -6383.9937
144.7454

WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 860000
WRITING COORDINATES TO DCD FILE AT STEP 860000
WRITING COORDINATES TO RESTART FILE AT STEP 860000
FINISHED WRITING RESTART COORDINATES
WRITING VELOCITIES TO RESTART FILE AT STEP 860000
FINISHED WRITING RESTART VELOCITIES
LDB: LOAD: AVG 54.73 MAX 61.5 MSGS: TOTAL 54 MAXC 36 MAXP 1 None
LDB: LOAD: AVG 54.73 MAX 55.67 MSGS: TOTAL 54 MAXC 36 MAXP 1 Refine

Step "0" of the second simulation:

ENERGY: 860000 3709.6487 5116.2603 2992.5012
6.9423 -18110.9999 -9771.7462 0.0000 0.0000
12444.8849 -3452.5088 144.6901 -3343.9650 -3343.9650
144.6901

The electrostatic energy is different (-18110.9999 instead of -21150.7474)
and I don't understand what is wrong !
My system configuration is:
- Dual AMD Athlon MP 2200
- Windows 2000
- NAMD 2.5 for Windows
At the end of this e-mail, you can find the input files for the two
simulations.
Thank you

        Alessandro Pedretti

--
Dr. Alessandro Pedretti
Ist. di Chimica Farmaceutica e Tossicologica
Viale Abruzzi, 42
I-20131 Milano (Italy)
Tel. +39 02 503 17522
Fax +39 02 503 17565
E-Mail: alessandro.pedretti_at_unimi.it
WWW: http://www.ddl.unimi.it
================================================================
This is the first aborted dynamics file input:
# Protocol params
numsteps  1000000
# Initial config
coordinates  a1aa_adre_mem_aq_min.pdb
temperature  300K
seed   12345
# Output params
outputname   a1aa_adre_mem_aq_dyn
outputEnergies   5000
outputtiming     5000
binaryoutput  yes
DCDFreq          5000
restartFreq      5000
# Integrator params
timestep  1.0
nonbondedFreq    2
fullElectFrequency  4
# Force field params
structure  a1aa_adre_mem_aq_min.psf
paraTypeCharmm   on
parameters  ../LIP/par_all22_prot_lipid.inp
exclude   scaled1-4
1-4scaling  0.4
switching  on
switchdist  8.0
cutoff   12.0
pairlistdist  14.0
margin   0.0
stepspercycle    20
# Cylindrical PBC
cylindricalBC           on
cylindricalBCCenter     0.0 0.0 0.0
cylindricalBCAxis       y
cylindricalBCr1         42.00
cylindricalBCl1         62.00
cylindricalBCk1         2
================================================================
... and this is the restart file:
set MolFile  a1aa_adre_mem_aq_dyn
set ResSuffix           2
set ParFile             ../LIP/par_all22_prot_lipid.inp
set StartStep           860000
set Steps               1500000
set Refresh             5000
# Please remember that "Steps" must be the sum of steps of the first
dynamics
# and the steps of the second one.
# End of user parameters
numsteps                $Steps
seed   12345
coordinates             a1aa_adre_mem_aq_dyn.restart.pdb
bincoordinates   $MolFile.restart.coor
binvelocities    $MolFile.restart.vel
extendedsystem          $MolFile.restart.xsc
outputname              $MolFile$ResSuffix
outputEnergies          $Refresh
binaryoutput            yes
DCDFreq                 $Refresh
restartFreq             $Refresh
firsttimestep           $StartStep
timestep                1.0
nonbondedFreq           2
fullElectFrequency      4
structure               a1aa_adre_mem_aq_min.psf
paraTypeCharmm          on
parameters              $ParFile
exclude                 scaled1-4
1-4scaling              1.0
switching               on
switchdist              8.0
cutoff                  12.0
pairlistdist            14.0
margin                  0.0
stepspercycle           20
# Cylindrical PBC
cylindricalBC           on
cylindricalBCCenter     0.0 0.0 0.0
cylindricalBCAxis       y
cylindricalBCr1         42.00
cylindricalBCl1         62.00
cylindricalBCk1         2
================================================================

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