Hi,
We recently updated from AMBER 22 to AMBER 24. I started an MD with
pmemd.cuda of AMBER 22 (it ran normally for many microseconds) then I
switched to pmemd.cuda of AMBER 24. As soon as I made the change, the
density started decreasing and the system became unstable. I am attaching
the output of energies that I got from both AMBER 22 and 24. There was no
change in input parameters. GPU was also of the same type for both runs. I
have tried multiple runs and problem repeats. The issue is not unique to
this protein as othr MD runs also face similar issue. Is there some change
in the new pmemd.cuda that is causing this. How can I resolve this.
######################AMBER 22###########################################
-------------------------------------------------------
Amber 22 PMEMD 2022
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 22
| Compiled date/time: Thu Apr 14 14:06:37 2022
| Run on 08/14/2024 at 12:17:56
...
...
...
NSTEP = 4990000 TIME(PS) =15050931.677 TEMP(K) = 300.25 PRESS =
0.0
Etot = -79808.8001 EKtot = 18418.2969 EPtot =
-98227.0970
BOND = 532.8799 ANGLE = 1404.0084 DIHED =
2212.8616
1-4 NB = 617.2352 1-4 EEL = 6508.8938 VDWAALS =
11504.5300
EELEC = -121015.0325 EHBOND = 0.0000 RESTRAINT =
7.5266
EAMBER (non-restraint) = -98234.6236
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
302156.8361
Density =
1.0206
------------------------------------------------------------------------------
NMR restraints: Bond = 7.130 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 5000000 TIME(PS) =15050951.677 TEMP(K) = 298.32 PRESS =
0.0
Etot = -80221.3986 EKtot = 18299.6211 EPtot =
-98521.0197
BOND = 537.9886 ANGLE = 1381.3407 DIHED =
2239.2079
1-4 NB = 645.6774 1-4 EEL = 6579.2741 VDWAALS =
11381.4582
EELEC = -121289.3481 EHBOND = 0.0000 RESTRAINT =
3.3814
EAMBER (non-restraint) = -98524.4011
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
300765.8277
Density =
1.0253
------------------------------------------------------------------------------
NMR restraints: Bond = 3.648 Angle = 0.000 Torsion = 0.000
===============================================================================
A V E R A G E S O V E R 500 S T E P S
NSTEP = 5000000 TIME(PS) =15050951.677 TEMP(K) = 300.10 PRESS =
0.0
Etot = -80147.5386 EKtot = 18408.7592 EPtot =
-98556.2977
BOND = 534.2904 ANGLE = 1425.3675 DIHED =
2212.2829
1-4 NB = 629.8769 1-4 EEL = 6554.3098 VDWAALS =
11527.2467
EELEC = -121443.9399 EHBOND = 0.0000 RESTRAINT =
4.2678
EAMBER (non-restraint) = -98560.5655
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
301146.2687
Density =
1.0240
------------------------------------------------------------------------------
NMR restraints: Bond = 3.648 Angle = 0.000 Torsion = 0.000
===============================================================================
R M S F L U C T U A T I O N S
NSTEP = 5000000 TIME(PS) =15050951.677 TEMP(K) = 1.74 PRESS =
0.0
Etot = 186.0862 EKtot = 106.8476 EPtot =
149.9055
BOND = 19.1396 ANGLE = 29.2437 DIHED =
16.2995
1-4 NB = 10.6081 1-4 EEL = 32.3977 VDWAALS =
153.7168
EELEC = 242.6810 EHBOND = 0.0000 RESTRAINT =
1.4702
EAMBER (non-restraint) = 148.4353
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
780.3742
Density =
0.0027
------------------------------------------------------------------------------
####################################################################################
######################AMBER
24######################################################
-------------------------------------------------------
Amber 24 PMEMD 2024
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 24
| Compiled date/time: Sun Jul 21 15:32:15 2024
| Run on 08/23/2024 at 12:54:39
..
..
..
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
| MC Barostat: Increasing size of volume moves
NSTEP = 10000 TIME(PS) =15050972.000 TEMP(K) = 303.67 PRESS =
0.0
Etot = -79540.7204 EKtot = 18628.0996 EPtot =
-98168.8200
BOND = 552.8356 ANGLE = 1482.7589 DIHED =
2212.7748
1-4 NB = 592.1929 1-4 EEL = 6485.2707 VDWAALS =
19690.1988
EELEC = -129190.2539 EHBOND = 0.0000 RESTRAINT =
5.4021
EAMBER (non-restraint) = -98174.2221
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
404869.3772
Density =
0.7617
------------------------------------------------------------------------------
NMR restraints: Bond = 4.906 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 20000 TIME(PS) =15050992.000 TEMP(K) = 303.02 PRESS =
0.0
Etot = -77219.4945 EKtot = 18588.0566 EPtot =
-95807.5511
BOND = 578.6448 ANGLE = 1448.6349 DIHED =
2233.2531
1-4 NB = 627.0087 1-4 EEL = 6478.6909 VDWAALS =
19011.3651
EELEC = -126191.7219 EHBOND = 0.0000 RESTRAINT =
6.5734
EAMBER (non-restraint) = -95814.1245
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
546801.2540
Density =
0.5640
------------------------------------------------------------------------------
NMR restraints: Bond = 6.149 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 30000 TIME(PS) =15051012.000 TEMP(K) = 301.97 PRESS =
0.0
Etot = -75715.3740 EKtot = 18523.8809 EPtot =
-94239.2549
BOND = 561.9478 ANGLE = 1451.4018 DIHED =
2223.0521
1-4 NB = 603.1276 1-4 EEL = 6458.0708 VDWAALS =
17056.5531
EELEC = -122601.3143 EHBOND = 0.0000 RESTRAINT =
7.9062
EAMBER (non-restraint) = -94247.1611
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
728786.3491
Density =
0.4231
------------------------------------------------------------------------------
NMR restraints: Bond = 7.906 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 40000 TIME(PS) =15051032.000 TEMP(K) = 300.00 PRESS =
0.0
Etot = -73929.2951 EKtot = 18402.7031 EPtot =
-92331.9983
BOND = 565.3402 ANGLE = 1479.1626 DIHED =
2242.7606
1-4 NB = 628.8603 1-4 EEL = 6515.2873 VDWAALS =
15912.6475
EELEC = -119679.7800 EHBOND = 0.0000 RESTRAINT =
3.7233
EAMBER (non-restraint) = -92335.7215
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
991203.1506
Density =
0.3111
------------------------------------------------------------------------------
NMR restraints: Bond = 3.637 Angle = 0.000 Torsion = 0.000
===============================================================================
######################################################################################
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Received on Fri Aug 23 2024 - 11:00:01 PDT
