Hi David,
If I print out every step, now RESTRAINT = NMR restraint, except for the last step.
NSTEP = 998 TIME(PS) = 1041.996 TEMP(K) = 300.69 PRESS = 0.0
Etot = -358897.1788 EKtot = 87884.1094 EPtot = -446781.2882
BOND = 1681.8092 ANGLE = 4932.0465 DIHED = 7056.8214
1-4 NB = 1986.2618 1-4 EEL = 30684.7727 VDWAALS = 58350.3441
EELEC = -551480.9630 EHBOND = 0.0000 RESTRAINT = 7.6191
EAMBER (non-restraint) = -446788.9073
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 1466443.0054
Density = 0.9974
------------------------------------------------------------------------------
NMR restraints: Bond = 7.619 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 999 TIME(PS) = 1041.998 TEMP(K) = 300.83 PRESS = 0.0
Etot = -358895.7469 EKtot = 87923.2500 EPtot = -446818.9969
BOND = 1711.7239 ANGLE = 4872.8643 DIHED = 7060.0508
1-4 NB = 1986.2559 1-4 EEL = 30690.4920 VDWAALS = 58341.6176
EELEC = -551489.7439 EHBOND = 0.0000 RESTRAINT = 7.7424
EAMBER (non-restraint) = -446826.7393
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 1466443.0054
Density = 0.9974
------------------------------------------------------------------------------
NMR restraints: Bond = 7.742 Angle = 0.000 Torsion = 0.000
===============================================================================
| MC Barostat: Decreasing size of volume moves
NSTEP = 1000 TIME(PS) = 1042.000 TEMP(K) = 300.91 PRESS = 0.0
Etot = -358898.3099 EKtot = 87947.5625 EPtot = -446845.8724
BOND = 1729.6946 ANGLE = 4818.1815 DIHED = 7068.6296
1-4 NB = 1986.3751 1-4 EEL = 30695.0660 VDWAALS = 58331.6058
EELEC = -551483.2410 EHBOND = 0.0000 RESTRAINT = 7.8161
EAMBER (non-restraint) = -446853.6885
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 1466443.0054
Density = 0.9974
------------------------------------------------------------------------------
NMR restraints: Bond = 117.324 Angle = 0.000 Torsion = 0.000
===============================================================================
I’m ot sure what happened on step 1000! That’s particularly true given what’s printed later:
Restraints, deviations, and energy contributions: pencut = 0.10
------------------------------------------------------------------------------
First atom Last atom curr. value target deviation penalty
------------------------------------------------------------------------------
*CA GLN 462 -- *CA GLN 154: 83.167 83.110 0.057 1.630 d 0: 0
*CA GLN 462 -- *CA GLN 308: 118.486 118.564 0.078 3.024 d 0: 0
*CA GLN 616 -- *CA GLN 308: 83.417 83.369 0.048 1.153 d 0: 0
*CA GLN 616 -- *CA GLN 154: 114.967 115.031 0.064 2.034 d 0: 0
Total distance penalty: 7.842
———————————————————————————————————————
The average is also different:
A V E R A G E S O V E R 1000 S T E P S
NSTEP = 1000 TIME(PS) = 1042.000 TEMP(K) = 300.03 PRESS = 0.0
Etot = -359081.7585 EKtot = 87689.2641 EPtot = -446771.0226
BOND = 1673.7687 ANGLE = 4938.8071 DIHED = 7084.8025
1-4 NB = 1968.0655 1-4 EEL = 30721.7319 VDWAALS = 58704.8740
EELEC = -551871.7450 EHBOND = 0.0000 RESTRAINT = 8.6727
EAMBER (non-restraint) = -446779.6953
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 1467091.1388
Density = 0.9970
------------------------------------------------------------------------------
NMR restraints: Bond = 117.324 Angle = 0.000 Torsion = 0.000
===============================================================================
The restraints look right. I’m also printing using a DUMPAVG file and everything looks reasonable there.
Still, out of curiosity, is there an averaging procedure that makes RESTRAINT not equal NMR restraint when some large number of steps are printed?
What happens on step 1000 so that these two values are not the same, at least in one part of the output?
I can share the relevant files if that would be useful.
Best,
Matthew
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Received on Wed Oct 26 2022 - 09:00:04 PDT
