Re: energy minimization in namd

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Thu Apr 23 2015 - 11:44:51 CDT

Hi Hasan,

Not sure about DX, DU and DUDX. However, you can verify whether your system
has minimized well by looking at the "TOTAL" energy (I believe it is column
12 in the lines beginning with ENERGY). If it has stabilized, then you are
good to get started. Usually 10000 steps provides enough minimization.

Chitrak.

wrote:

> Dear All,
>
> I run 10000 step energy minimization for my simulation system. The last
> part of my namd out file can be seen in below. What are DX , DU and DUDX
> in “LINE MINIMIZER BRACKET” line ? And How can I understand that 10000
> step energy minimization is enough or not to start equilibration ?
>
> Thanks for the explanation.
>
> ************
>
> LINE MINIMIZER BRACKET: DX 0.000236595 0.000674418 DU -0.015094 0.0970886
> DUDX -97.2742 2.11463 285.38
> PRESSURE: 9999 -573.684 -11.0714 1.23184 -11.0714 -539.603 14.7132 1.23184
> 14.7132 -162.05
> GPRESSURE: 9999 -572.433 -10.8975 1.2972 -11.0482 -538.393 14.5997 1.27755
> 14.7093 -160.769
> ENERGY: 9999 5759.6569 2577.9163 457.8570
> 0.0000 -132654.3270 25903.7601 0.0000 0.0000
> 0.0000 -97955.1366 0.0000 -97955.1366 -97955.1366
> 0.0000 -425.1123 -423.8652 1361250.0000
> -425.1123 -423.8652
>
> LINE MINIMIZER BRACKET: DX 2.36595e-05 0.000674418 DU -0.000307767
> 0.0970886 DUDX -7.82503 2.11463 285.38
> PRESSURE: 10000 -573.698 -11.0727 1.22639 -11.0727 -539.606 14.7258
> 1.22639 14.7258 -162.109
> GPRESSURE: 10000 -572.424 -10.8974 1.29553 -11.049 -538.377 14.6077
> 1.27498 14.7187 -160.804
> TIMING: 10000 CPU: 655.865, 0.0655963/step Wall: 655.865,
> 0.0655963/step, 0 hours remaining, 1873.847656 MB of memory in use.
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY MISC
> KINETIC TOTAL TEMP POTENTIAL TOTAL3
> TEMPAVG PRESSURE GPRESSURE VOLUME
> PRESSAVG GPRESSAVG
>
> ENERGY: 10000 5759.7022 2577.9230 457.8567
> 0.0000 -132654.3854 25903.7665 0.0000 0.0000
> 0.0000 -97955.1369 0.0000 -97955.1369 -97955.1369
> 0.0000 -425.1379 -423.8685 1361250.0000
> -425.1379 -423.8685
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 10000
> WRITING COORDINATES TO DCD FILE AT STEP 10000
> WRITING COORDINATES TO RESTART FILE AT STEP 10000
> FINISHED WRITING RESTART COORDINATES
> The last position output (seq=10000) takes 0.004 seconds, 1873.848 MB of
> memory in use
> WRITING VELOCITIES TO RESTART FILE AT STEP 10000
> FINISHED WRITING RESTART VELOCITIES
> The last velocity output (seq=10000) takes 0.003 seconds, 1873.848 MB of
> memory in use
> REINITIALIZING VELOCITIES AT STEP 10000 TO 309 KELVIN.
>
>
>

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