On Sun, Jul 12, 2020, Vishal Reddy wrote:
>
>Initially i had a system running in namd now i want to shift it into
>amber so i used chamber in parmed tool to generated prmtop and inpcrd
>files.
>
>Now to test the correctness of the prmtop and inpcrd, i have done a 5
>step minimization proces printing out the energies at each step and i
>found that only few(BOND,IMPRP)energies are matched precisely in both the
>softwares and few other (DIHED, ELECT) were close but not exact and other
>values like ENERGY were differed by large values.
This is kind of old, but has useful info on how to get simulations in
namd and Amber to match (using the same prmtop files). I'm not sure if
that is how you are making your comparison, or if you are using the
charmm files in namd and the converted prmtop in Amber. But, if you
haven't studied it, it might help:
https://ambermd.org/namd/namd_amber.html
>pasting the log file 2 steps of both namd and amber.
>
>AMBER
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 2.3700E+09 2.9256E+02 1.7382E+04 OH2 41312
>
> BOND = 16634.4131 ANGLE = 4241.5468 DIHED = 733.4648
> UB = 49.7639 IMP = 10.7682 CMAP = -25.1870
> VDWAALS = ************* EEL = -191890.9833 HBOND = 0.0000
> 1-4 VDW = 269.8868 1-4 EEL = 3063.0998 RESTRAINT = 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2 2.3440E+09 2.9246E+02 1.7404E+04 OH2 41312
>
> BOND = 16632.3664 ANGLE = 4241.2552 DIHED = 733.4645
> UB = 49.7611 IMP = 10.7677 CMAP = -25.1873
> VDWAALS = ************* EEL = -191892.6276 HBOND = 0.0000
> 1-4 VDW = 269.8849 1-4 EEL = 3063.0983 RESTRAINT = 0.0000
>
>NAMD
>ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
>
>ENERGY: 0 16634.4177 4291.3007 708.2777 10.7682 -189072.0783 3178866.8931 0.0000 0.0000 0.0000 3011439.5792 0.0000 3011439.5792 3011439.5792 0.0000 -20256.1931 62813.2161 573221.4051 -20256.1931 62813.2161
>
>ENERGY: 1 16635.4363 4290.8483 708.3914 11.0255 -189303.1727 1082894.1312 0.0000 0.0000 0.0000 915236.6600 0.0000 915236.6600 915236.6600 0.0000 -20253.2932 -5411.0473 573221.4051 -20253.2932 -5411.0473
>
It's probably best to start from a better structure: minimization with
such a large vdW energy (indicative of bad clashses) will certainly
diverge in the two codes. In fact, even in the best of circumstances,
the minimizers in NAMD and Amber are different, so only the initial
energies should be expected to match.
The fact that your Angle energies are different suggests that something
pretty bad is going on, though.
...dac
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Received on Sun Jul 12 2020 - 18:30:05 PDT
