From: Aron Broom (broomsday_at_gmail.com)
Date: Tue Jul 17 2012 - 17:34:38 CDT
I can't answer the part about the minimizer, but as a quick note concerning
your mentioning looking at differently protonated sites: if you are
thinking to use the POTENTIAL energy to decide which protonation
configuration is best, I think that will not work. You should use the
ELECT instead, as the full potential will be taking into account bond
parameters (dihedrals and such) which may not be relevant to the question
of which site is most favourable for protonation, but which will change
depending on which sidechain has the proton attached. By using just the
electrostatic potential, you will overcome this problem and have a better
sense of where it is most favourable to place a given charge, rather than
where it is most favourable to make a fake (since this is classical MD)
covalent bond.
Having said the above, I think minimization (at least this kind) is a bad
choice for comparing energies, because you ignore the whole ensemble of
states that are likely very close to the local or global minimum, and which
can be dramatically different between two charge configurations. I would
suggest equilibrating, and then, once the system has stabilized (by RMSD
for instance), take a number of snapshots along another window of
equilibration and then compare them (minimizing each snapshot if you
wish).
Just my two cents.
~Aron
On Tue, Jul 17, 2012 at 6:14 PM, Sándor Kovács <skovacs_at_wustl.edu> wrote:
> Greetings experts,
>
> I had a question about the minimization algorithm as implemented in NAMD.
>
> For a system of ~20,000 atoms, when starting from the same initial
> conditions (READ: same atomic positions), the first 5000 steps of my
> minimizations are IDENTICAL (as tested with diff).
> After this point, however, repeat trials begin to diverge from
> one-another, and result in POTENTIAL energies differing by as many as ±10
> kcal/mol after 50K minimization steps.
> These differences persist when the minimization is carried out for 200K
> steps (I wanted to make sure each had completely converged).
>
> e.g. for three separate trials after 5000 minimization steps, I obtain
> identical results:
>
> [TRIAL 1]
> TIMING: 5000 CPU: 184.51, 0.0350367/step Wall: 184.51, 0.0350367/step,
> 1.89782 hours remaining, 106.558594 MB of memory in use.
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY MISC
> KINETIC TOTAL TEMP POTENTIAL TOTAL3
> TEMPAVG
>
> ENERGY: 5000 1124.8303 4717.7323 3713.3759
> 139.7911 -34583.7700 -6281.9927 0.0000 0.0000
> 0.0000 -31170.0331 0.0000 -31170.0331
> -31170.0331 0.0000
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 5000
> LINE MINIMIZER BRACKET: DX 0.000499702 0.000999403 DU -0.0921908 0.16983
> DUDX -302.606 -66.3689 406.269
>
>
> [TRIAL 2]
> TIMING: 5000 CPU: 184.356, 0.0350742/step Wall: 184.356, 0.0350742/step,
> 1.89985 hours remaining, 106.617188 MB of memory in use.
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY MISC
> KINETIC TOTAL TEMP POTENTIAL TOTAL3
> TEMPAVG
>
> ENERGY: 5000 1124.8303 4717.7323 3713.3759
> 139.7911 -34583.7701 -6281.9927 0.0000 0.0000
> 0.0000 -31170.0331 0.0000 -31170.0331
> -31170.0331 0.0000
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 5000
>
>
> [TRIAL 3]
> TIMING: 5000 CPU: 184.478, 0.035129/step Wall: 184.478, 0.035129/step,
> 1.90282 hours remaining, 106.367188 MB of memory in use.
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY MISC
> KINETIC TOTAL TEMP POTENTIAL TOTAL3
> TEMPAVG
>
> ENERGY: 5000 1124.8303 4717.7324 3713.3759
> 139.7911 -34583.7702 -6281.9926 0.0000 0.0000
> 0.0000 -31170.0331 0.0000 -31170.0331
> -31170.0331 0.0000
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 5000
> LINE MINIMIZER BRACKET: DX 0.000499698 0.000999396 DU -0.0921886 0.169841
> DUDX -302.606 -66.363 406.287
>
>
> after 50K minimization steps, one sees a divergence in the tens place:
>
> [TRIAL 1]
> LINE MINIMIZER BRACKET: DX 0.000511803 9.74047e-05 DU -0.000141415
> 5.12214e-06 DUDX -0.552612 3.6656e-08 0.105172
> LINE MINIMIZER REDUCING GRADIENT FROM 1.15801 TO 0.00115801
> TIMING: 50000 CPU: 1784.96, 0.0353003/step Wall: 1784.96,
> 0.0353003/step, 1.47085 hours remaining, 106.535156 MB of memory in use.
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY MISC
> KINETIC TOTAL TEMP POTENTIAL TOTAL3
> TEMPAVG
>
> ENERGY: 50000 1129.8369 4769.8503 3772.9891
> 142.4910 -35065.8099 -6378.5568 0.0000 0.0000
> 0.0000 -31629.1995 0.0000 *-31629.1995*
> -31629.1995 0.0000
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 50000
>
> [TRIAL 2]
> LINE MINIMIZER BRACKET: DX 0.000580501 0.001161 DU -0.000380669 0.0010312
> DUDX -1.1704 -0.141114 1.91753
> TIMING: 50000 CPU: 1773.21, 0.0352761/step Wall: 1773.21,
> 0.0352761/step, 1.46984 hours remaining, 106.558594 MB of memory in use.
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY MISC
> KINETIC TOTAL TEMP POTENTIAL TOTAL3
> TEMPAVG
>
> ENERGY: 50000 1129.6438 4771.2127 3764.2485
> 140.6916 -35041.1554 -6374.3260 0.0000 0.0000
> 0.0000 -31609.6847 0.0000 *-31609.6847*
> -31609.6847 0.0000
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 50000
>
> [TRIAL 3]
> LINE MINIMIZER BRACKET: DX 0.000196034 0.000856693 DU -0.00200314
> 0.0381771 DUDX -20.3922 -0.0399876 89.2622
> LINE MINIMIZER REDUCING GRADIENT FROM 123.878 TO 0.123878
> TIMING: 50000 CPU: 1836.9, 0.0352672/step Wall: 1836.9, 0.0352672/step,
> 1.46947 hours remaining, 107.398438 MB of memory in use.
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY MISC
> KINETIC TOTAL TEMP POTENTIAL TOTAL3
> TEMPAVG
>
> ENERGY: 50000 1128.4327 4767.2091 3765.5526
> 139.9726 -35046.9333 -6368.0236 0.0000 0.0000
> 0.0000 -31613.7900 0.0000 *-31613.7900*
> -31613.7900 0.0000
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 50000
>
>
> and after 200K minimization steps (to ensure convergence to a local
> minima), the differences remain:
>
> [TRIAL 1]
> LINE MINIMIZER BRACKET: DX 5.58613e-05 0.000330726 DU -2.54659e-11
> 4.00178e-11 DUDX 2.62465e-08 3.68785e-08 9.98249e-08
> TIMING: 200000 CPU: 7113.24, 0.0353183/step Wall: 7113.24,
> 0.0353183/step, 0 hours remaining, 107.148438 MB of memory in use.
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY MISC
> KINETIC TOTAL TEMP POTENTIAL TOTAL3
> TEMPAVG
>
> ENERGY: 200000 1129.1383 4765.1845 3784.9412
> 142.4877 -35093.0615 -6379.9375 0.0000 0.0000
> 0.0000 -31651.2473 0.0000 -31651.2473
> -31651.2473 0.0000
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 200000
>
> [TRIAL 2]
> LINE MINIMIZER BRACKET: DX 0.000907904 0.000907904 DU -7.80979e-07
> 5.97607e-07 DUDX -0.00161935 -0.000100987 0.00141738
> TIMING: 200000 CPU: 7119.27, 0.0355447/step Wall: 7119.27,
> 0.0355447/step, 0 hours remaining, 107.281250 MB of memory in use.
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY MISC
> KINETIC TOTAL TEMP POTENTIAL TOTAL3
> TEMPAVG
>
> ENERGY: 200000 1130.0652 4766.4965 3776.1033
> 141.0543 -35082.0893 -6370.2935 0.0000 0.0000
> 0.0000 -31638.6636 0.0000 -31638.6636
> -31638.6636 0.0000
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 200000
>
> [TRIAL 3]
> TIMING: 200000 CPU: 7281.36, 0.0350886/step Wall: 7281.36,
> 0.0350886/step, 0 hours remaining, 107.398438 MB of memory in use.
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY MISC
> KINETIC TOTAL TEMP POTENTIAL TOTAL3
> TEMPAVG
>
> ENERGY: 200000 1129.6536 4770.1929 3775.7018
> 141.1868 -35087.2720 -6374.7239 0.0000 0.0000
> 0.0000 -31645.2607 0.0000 -31645.2607
> -31645.2607 0.0000
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 200000
>
>
> I thought the minimization procedure was deterministic--i.e. repeat trials
> should all converge to the same energy minimum (ideally the global one, but
> I understand that they can be 'stuck' in local minima).
> Is there something going on (stochastic, perhaps) during the minimization
> procedure which would account for this discrepancy?
>
> Alternatively, is there a better procedure I should be following If I
> would like to obtain an estimate of the system's potential energy for
> comparison to similar systems with, say, slightly differently protonated
> sites?
>
> I can make input files available off-list if someone needs to reproduce
> the above.
>
> Thanks,
> Sándor
> ________________________________________________________
> Sándor Ádám Kovács, B.S. M.S.
> President, Association of Graduate Engineering Students (AGES)
> Ph.D. Candidate and Graduate Research Assistant
> Department of Energy, Environmental and Chemical Engineering
> Washington University in St. Louis -- St. Louis, MO 63130 -- U.S.A.
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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