Hello Everyone,
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.
Is it ok to ignore the difference and use the generated prmtop file or is there a way to match them precisely.
link with log files and config files : https://drive.google.com/drive/folders/107JVYPnsy9_qED9ifakcKvyNE7QX8LhC?usp=sharing
Please suggest how can i proceed furthur.
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
THANKS
Vishal
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Received on Sun Jul 12 2020 - 14:30:03 PDT
