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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