Dear Amber users,
I was doing TMD simulation for a small protein of 120 amino acids. The force constant (TGRMDFRC) I was using is 2. I was applying restrain force on all the heavy atoms (NTTGTRMS = 953) but aligning the structure with the reference structure based on their C* trace (120 C* atoms). I was trying to calculate the Restrain potential from the following equation in the Amber10 manual:
E = 0.5 * TGTMDFRC * NATTGTRMS * (RMSD-TGTRMSD)**2
If I calculate the restraint energy (RESTRAINT) for the given example and they come out to be slightly different (1.3761 and 2.0165 compared to 1.3443 and 2.0047 respectively). I have considered RMSD as "Current RMSD from reference" and TGTRMSD as "Current target RMSD" (please see the example below). Why there is such deviation? I guess it is not truncation error or something like that.
Thank you for your input.
With best regards,
Rahul Banerjee
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 100 TIME(PS) = 0.200 TEMP(K) = 281.47 PRESS = 78.8
Etot = -59693.3975 EKtot = 13225.6527 EPtot = -72919.0502
BOND = 344.6748 ANGLE = 917.0819 DIHED = 1246.7549
1-4 NB = 437.6376 1-4 EEL = 6023.0834 VDWAALS = 9689.5997
EELEC = -91579.2268 EHBOND = 0.0000 RESTRAINT = 1.3443
EAMBER (non-restraint) = -72920.3945
EKCMT = 5952.4662 VIRIAL = 5561.2691 VOLUME = 229880.0226
Density = 1.0182
Ewald error estimate: 0.7172E-04
Current RMSD from reference: 0.788
Current target RMSD: 0.750
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 150 TIME(PS) = 0.300 TEMP(K) = 294.87 PRESS = 118.7
Etot = -58177.1508 EKtot = 13855.3267 EPtot = -72032.4775
BOND = 367.8662 ANGLE = 962.7299 DIHED = 1283.7928
1-4 NB = 447.1210 1-4 EEL = 6022.8517 VDWAALS = 9476.6759
EELEC = -90595.5197 EHBOND = 0.0000 RESTRAINT = 2.0047
EAMBER (non-restraint) = -72034.4822
EKCMT = 6235.2483 VIRIAL = 5646.1869 VOLUME = 229936.7782
Density = 1.0179
Ewald error estimate: 0.6539E-05
Current RMSD from reference: 0.796
Current target RMSD: 0.750
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Received on Fri Apr 08 2011 - 11:00:06 PDT
