From: Fangqiang Zhu (fzhu_at_ks.uiuc.edu)
Date: Thu Nov 20 2003 - 17:15:11 CST
Hi,
I think your simulation was intended to be of vacuum type (i.e., not
periodic).
Therefore, in your restart simulation, you shouldn't specify "extendedsystem".
When that command is present, NAMD will do the simulation with periodic
boundary condition, and that's why you see different electrostatic energy.
Zhu
Alessandro Pedretti wrote:
> 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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