Re: Energy problem after restart

From: Alessandro Pedretti (alessandro.pedretti_at_unimi.it)
Date: Mon Nov 24 2003 - 03:00:11 CST

Thank you for the answer !
I removed the line:

extendedsystem $MolFile.restart.xsc

from the resatart file, but the problem is still present: the electrostatic
energy is undersetimated. After the restart, it seems that the dielectric
constants is changed from 1 to 1.17, but it's funny !

    Alessandro

----- Original Message -----
From: "Fangqiang Zhu" <fzhu_at_ks.uiuc.edu>
To: "Alessandro Pedretti" <alessandro.pedretti_at_unimi.it>
Cc: <namd-l_at_ks.uiuc.edu>
Sent: Friday, November 21, 2003 12:15 AM
Subject: Re: namd-l: Energy problem after restart

> 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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