From: snoze pa (snoze.pa_at_gmail.com)
Date: Fri Feb 10 2006 - 15:24:25 CST
Did you notice that now you are heating the system. Till elec=-13487.2964 ,
you were minimizing the system and after that your system temperature is
increased from 0 to 17.9442 K and so on.
On 2/10/06, M. Madhu <madhu7_at_hotmail.com> wrote:
>
>
> Dear All,
>
> I am doing the tutorial - Gramicidin in explicit membrane (pope/water)
> system - which is available at the following website:
>
> http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on
>
> I notice jumps in electrostatic energy between two values when I do the
> equilibration (../../namd2 equil.namd).
>
> The results are same either I use the original grama.psf, grama.pdb,
> fix_backbone.pdb and restrain_ca.pdb or my own *.pdb and *psf files.
> In both cases, I used the correct parameter (par_all27_prot_lipid.inp,
> par-extraterms.inp) and topology (frotop_all27_prot_lipid.inp) files and
> the same equil.namd file from the above website.
>
> I tried different versions of namd (NAMD_2.5b1_Linux-i686,
> NAMD_2.6b1_Linux-i686 and NAMD_2.6b1_Linux-i686-TCP)
> on a linux machine, and also NAMD with Myrnet MX on MacOSX
> (both serial and parallel). In all the cases, I observed the same probelm.
>
> I will attach the equil.namd and a portion of the output file at the end
> of
> this message for your reference.
>
> Can someone explain why this is happening? Did anyone observe this
> kind of behavior? Am I doing something wrong?
>
> Thanks a lot.
> Madhu
> ==================================================
>
> ------
> equil.namd (original)
> ------
>
> structure grama.psf
> coordinates grama.pdb
> temperature 0
> parameters par_all27_prot_lipid.inp
> parameters par-extraterms.inp
> paraTypeCharmm on
>
> outputEnergies 10
> outputTiming 100
> xstFreq 100
> dcdFreq 100
> wrapAll on
> wrapNearest on
>
> timestep 1
> nonBondedFreq 2
> fullElectFrequency 4
> stepsPerCycle 20
>
> switching on
> switchDist 8.5
> cutoff 10
> pairlistdist 11.5
>
> cellBasisVector1 30.00 00.00 00.00
> cellBasisVector2 15.00 25.98 00.00
> cellBasisVector3 00.00 00.00 64.00
> # the z dimension is going to shrink so pad sufficiently
> # the margin could be reduced once the cell is equilibrated
> margin 5
>
> Pme on
> PmeGridsizeX 32
> PmeGridsizeY 32
> PmeGridsizeZ 64
>
> exclude scaled1-4
> 1-4scaling 1.0
>
> fixedAtoms on
> fixedAtomsForces on
> fixedAtomsFile fix_backbone.pdb
> fixedAtomsCol B
>
> constraints on
> consRef restrain_ca.pdb
> consKFile restrain_ca.pdb
> consKCol B
>
> langevin on
> langevinDamping 10
> langevinTemp 310
> langevinHydrogen no
>
> langevinPiston on
> langevinPistonTarget 1.01325
> langevinPistonPeriod 200
> langevinPistonDecay 100
> langevinPistonTemp 310
>
> useGroupPressure yes # smaller fluctuations
> useFlexibleCell yes # allow dimensions to fluctuate
> independently
> useConstantRatio yes # fix shape in x-y plane
>
> binaryoutput off
> outputname equil_out
>
> # run one step to get into scripting mode
> minimize 0
>
> # turn off until later
> langevinPiston off
>
> # minimize nonbackbone atoms
> minimize 1000
> output min_fix
>
> # min all atoms
> fixedAtoms off
> minimize 1000
> output min_all
>
> # heat with CAs restrained
> # langevin on
> run 3000
> output heat
>
> # equilibrate volume with CAs restrained
> langevinPiston on
> run 5000
> output equil_ca
>
> # equilibrate volume without restraints
> constraintScaling 0
> run 10000
> ===============================================
>
> --------------
> output file
> --------------
>
> Until 2000 step, electrostatic energy is pretty stable. After that it
> jumps between two average values (initially) (~ -13500 and ! -72000).
> Towards the end of the simulation, electrostatic energies were:
>
> 19990 (step no) -70034.7626 (elec)
> 20000 (step no) -11584.1788 (elec)
> ----
> -------
> ETITLE: TS
> BOND ANGLE DIHED IMPRP
> ELECT VDW BOUNDARY
> MISC KINETIC
> TOTAL TEMP TOTAL2
> TOTAL3 TEMPAVG
> PRESSURE GPRESSURE VOLUME
> PRESSAVG GPRESSAVG
> -----
> ENERGY: 1995 418.2656 720.4155 526.1334
> 4.8189
> -13486.2315 773.9508 14.4432 0.0000
> 0.0000
> -11028.2039 0.0000 -11028.2039 -11028.2039
> 0.0000
> -300.8747 -261.6859 49881.6000 -300.8747 -
> 261.6859
>
> BRACKET: 3.90647e-08 9.13854e-06 -5.59563 -5.43265 -5.28618
> ENERGY: 1996 418.2656 720.4155 526.1334
> 4.8189
> -13486.2314 773.9509 14.4432 0.0000
> 0.0000
> -11028.2039 0.0000 -11028.2039 -11028.2039
> 0.0000
> -300.8747 -261.6856 49881.6000 -300.8747 -
> 261.6856
>
> BRACKET: 2.24108e-08 1.40932e-05 -5.59563 -5.43265 -5.41802
> ENERGY: 1997 418.2656 720.4155 526.1334
> 4.8189
> -13486.2315 773.9509 14.4432 0.0000
> 0.0000
> -11028.2039 0.0000 -11028.2039 -11028.2039
> 0.0000
> -300.8747 -261.6856 49881.6000 -300.8747 -
> 261.6856
>
> BRACKET: 2.07454e-08 9.13854e-06 -5.59563 -5.43265 -5.43134
> ENERGY: 1998 418.2656 720.4155 526.1334
> 4.8189
> -13486.2315 773.9509 14.4432 0.0000
> 0.0000
> -11028.2039 0.0000 -11028.2039 -11028.2039
> 0.0000
> -300.8747 -261.6855 49881.6000 -300.8747 -
> 261.6855
>
> BRACKET: 1.85043e-10 1.4288e-06 -5.43265 -5.43274 -5.43134
> NEW SEARCH DIRECTION
> INITIAL STEP: 0.004096
> GRADIENT TOLERANCE: 0.949101
> ENERGY: 1999 417.6860 719.5507 526.0009
> 4.7204
> -13487.2964 772.6279 14.5145 0.0000
> 0.0000
> -11032.1961 0.0000 -11032.1961 -11032.1961
> 0.0000
> -279.4100 -264.4487 49881.6000 -279.4100 -
> 264.4487
>
>
> TIMING: 2000 CPU: 199.964, 0.0937059/step Wall: 205.708, 0.0953566/step,
> 0
> hours remaining, 0 kB of memory in use.
> ETITLE: TS
> BOND ANGLE DIHED IMPRP
> ELECT VDW BOUNDARY
> MISC KINETIC
> TOTAL TEMP TOTAL2
> TOTAL3 TEMPAVG
> PRESSURE GPRESSURE VOLUME
> PRESSAVG GPRESSAVG
>
> ENERGY: 2000 417.6860 719.5507 526.0009
> 4.7204
> -13487.2964 772.6279 14.5145 0.0000
> 0.0000
> -11032.1961 0.0000 -11032.1961 -11032.1961
> 0.0000
> -279.4100 -264.4487 49881.6000 -279.4100 -
> 264.4487
>
> WRITING COORDINATES TO DCD FILE AT STEP 2000
> TCL: Writing to files with basename min_all.
> WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 2000
> WRITING COORDINATES TO OUTPUT FILE AT STEP 2000
> WRITING VELOCITIES TO OUTPUT FILE AT STEP 2000
> TCL: Running for 3000 steps
> ETITLE: TS
> BOND ANGLE DIHED IMPRP
> ELECT VDW BOUNDARY
> MISC KINETIC
> TOTAL TEMP TOTAL2
> TOTAL3 TEMPAVG
> PRESSURE GPRESSURE VOLUME
> PRESSAVG GPRESSAVG
>
> ENERGY: 2000 417.6860 719.5507 526.0009
> 4.7204
> -13487.2964 772.6279 14.5145 0.0000
> 0.0000
> -11032.1961 0.0000 -11016.7962 -11074.5459
> 0.0000
> -236.4965 -264.2065 49881.6000 -236.4965 -
> 264.2065
>
> OPENING EXTENDED SYSTEM TRAJECTORY FILE
> ENERGY: 2010 449.4838 714.3638 525.1769
> 5.4026
> -72003.1496 780.0406 14.5464 0.0000
> 266.6365
> -69247.4990 17.9442 -69236.6451 -69269.7547
> 10.8347
> 20.2634 -10.0813 49881.6000 -6.5605 -
> 26.5967
>
> ENERGY: 2020 471.1117 774.7314 524.6428
> 6.4140
> -13509.7339 817.1226 14.4913 0.0000
> 465.3746
> -10435.8454 31.3189 -10423.8931 -10453.5553
> 25.8458
> 265.8635 179.3526 49881.6000 187.4143
> 183.6712
>
> ENERGY: 2030 489.2160 785.2061 527.0358
> 8.2814
> -71995.7303 867.0948 14.5662 0.0000
> 611.0464
> -68693.2836 41.1224 -68681.7813 -68704.0492
> 36.6506
> 798.2396 711.1190 49881.6000 634.4276
> 623.4282
>
> ENERGY: 2040 503.1644 845.9927 532.9298
> 9.0437
> -13466.3974 895.4291 14.6827 0.0000
> 714.3774
> -9950.7777 48.0764 -9937.1276 -9960.9020
> 45.1187
> 1142.6115 940.9986 49881.6000 918.9373
> 902.8902
>
> ENERGY: 2050 524.4092 862.7867 540.6675
> 10.1591
> -71942.2701 910.4502 14.5249 0.0000
> 858.8665
> -68220.4058 57.8002 -68206.5239 -68226.6751
> 53.9869
> 1542.6448 1367.3536 49881.6000 1255.8167
> 1259.8305
>
> this pattern goes on till the end of the run.
> -------
>
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