Re: Minimization Crashing Implicit Solvent

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Fri Feb 18 2022 - 16:49:04 CST

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Ok, I tried using NAMD 2.13 instead of NAMD 2.15alpha and the minimization works now in implicit solvent. Not sure why NAMD 2.15alpha doesn't work...

Dr. Kelly L. McGuire

PhD Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of McGuire, Kelly <mcg05004_at_byui.edu>
Sent: Friday, February 18, 2022 1:30 PM
To: namd-l_at_ks.uiuc.edu <namd-l_at_ks.uiuc.edu>
Subject: namd-l: Minimization Crashing Implicit Solvent

I haven't used implicit solvent in my simulations, usually explicit and everything works there. But when I try to minimize my protein complex in implicit solvent, it crashes after a few steps. I haven't seen this before. Why is the energy rising quickly and then crash?

CL: Minimizing for 2000 steps
PRESSURE: 0 0 0 0 0 0 0 0 0 0
GPRESSURE: 0 0 0 0 0 0 0 0 0 0
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG

ENERGY: 0 1044.8181 1843.1361 4501.2444 83.6584 -17830.8731 1341346.9282 0.0000 0.0000 0.0000 1330988.9121 0.0000 1330988.9121 1330988.9121 0.0000

OPENING EXTENDED SYSTEM TRAJECTORY FILE
MINIMIZER SLOWLY MOVING 66 ATOMS WITH BAD CONTACTS DOWNHILL
PRESSURE: 1 0 0 0 0 0 0 0 0 0
GPRESSURE: 1 0 0 0 0 0 0 0 0 0
ENERGY: 1 1115.1032 1874.9481 4504.2886 85.3061 -99999999999.9999 540932.3214 0.0000 0.0000 0.0000 -99999999999.9999 0.0000 -99999999999.9999 -99999999999.9999 0.0000

MINIMIZER SLOWLY MOVING 50 ATOMS WITH BAD CONTACTS DOWNHILL
PRESSURE: 2 0 0 0 0 0 0 0 0 0
GPRESSURE: 2 0 0 0 0 0 0 0 0 0
ENERGY: 2 1275.5324 1934.9848 4509.7841 87.8000 -99999999999.9999 207752.9878 0.0000 0.0000 0.0000 -99999999999.9999 0.0000 -99999999999.9999 -99999999999.9999 0.0000

MINIMIZER SLOWLY MOVING 29 ATOMS WITH BAD CONTACTS DOWNHILL
PRESSURE: 3 0 0 0 0 0 0 0 0 0
GPRESSURE: 3 0 0 0 0 0 0 0 0 0
ENERGY: 3 1418.8151 1984.1332 4515.2527 91.2703 -99999999999.9999 119878.6110 0.0000 0.0000 0.0000 -99999999999.9999 0.0000 -99999999999.9999 -99999999999.9999 0.0000

MINIMIZER SLOWLY MOVING 19 ATOMS WITH BAD CONTACTS DOWNHILL
PRESSURE: 4 0 0 0 0 0 0 0 0 0
GPRESSURE: 4 0 0 0 0 0 0 0 0 0
ENERGY: 4 1533.9009 2029.6843 4522.1144 95.9432 -99999999999.9999 104338.3966 0.0000 0.0000 0.0000 -99999999999.9999 0.0000 -99999999999.9999 -99999999999.9999 0.0000

MINIMIZER SLOWLY MOVING 10 ATOMS WITH BAD CONTACTS DOWNHILL
PRESSURE: 5 0 0 0 0 0 0 0 0 0
GPRESSURE: 5 0 0 0 0 0 0 0 0 0
ENERGY: 5 1629.9359 2061.2148 4528.2774 98.0353 -99999999999.9999 92608.7991 0.0000 0.0000 0.0000 -99999999999.9999 0.0000 -99999999999.9999 -99999999999.9999 0.0000

MINIMIZER SLOWLY MOVING 7 ATOMS WITH BAD CONTACTS DOWNHILL
PRESSURE: 6 0 0 0 0 0 0 0 0 0
GPRESSURE: 6 0 0 0 0 0 0 0 0 0
ENERGY: 6 1703.3638 2078.7444 4531.1776 101.2994 -99999999999.9999 26321.1100 0.0000 0.0000 0.0000 -99999999999.9999 0.0000 -99999999999.9999 -99999999999.9999 0.0000

MINIMIZER SLOWLY MOVING 4 ATOMS WITH BAD CONTACTS DOWNHILL
PRESSURE: 7 0 0 0 0 0 0 0 0 0
GPRESSURE: 7 0 0 0 0 0 0 0 0 0
ENERGY: 7 1720.5819 2087.1430 4534.3248 101.2994 -99999999999.9999 11945.1061 0.0000 0.0000 0.0000 -99999999999.9999 0.0000 -99999999999.9999 -99999999999.9999 0.0000

MINIMIZER SLOWLY MOVING 2 ATOMS WITH BAD CONTACTS DOWNHILL
PRESSURE: 8 0 0 0 0 0 0 0 0 0
GPRESSURE: 8 0 0 0 0 0 0 0 0 0
ENERGY: 8 1740.8792 2093.4587 4537.5554 101.2994 -99999999999.9999 8567.2025 0.0000 0.0000 0.0000 -99999999999.9999 0.0000 -99999999999.9999 -99999999999.9999 0.0000

MINIMIZER SLOWLY MOVING 2 ATOMS WITH BAD CONTACTS DOWNHILL
PRESSURE: 9 0 0 0 0 0 0 0 0 0
GPRESSURE: 9 0 0 0 0 0 0 0 0 0
ENERGY: 9 1763.6558 2100.6111 4540.8000 101.2994 -99999999999.9999 7680.0330 0.0000 0.0000 0.0000 -99999999999.9999 0.0000 -99999999999.9999 -99999999999.9999 0.0000

LDB: ============= START OF LOAD BALANCING ============== 3.0499
LDB: ============== END OF LOAD BALANCING =============== 3.05009
Info: useSync: 0 useProxySync: 0
LDB: =============== DONE WITH MIGRATION ================ 3.05017
MINIMIZER SLOWLY MOVING 2 ATOMS WITH BAD CONTACTS DOWNHILL
PRESSURE: 10 0 0 0 0 0 0 0 0 0
GPRESSURE: 10 0 0 0 0 0 0 0 0 0
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG

ENERGY: 10 1785.6340 2107.0483 4544.1467 101.2994 -17840.8561 7385.4353 0.0000 0.0000 0.0000 -1917.2925 0.0000 -1917.2925 -1917.2925 0.0000

MINIMIZER STARTING CONJUGATE GRADIENT ALGORITHM
LINE MINIMIZER REDUCING GRADIENT FROM 1.50758e+08 TO 150758
PRESSURE: 11 0 0 0 0 0 0 0 0 0
GPRESSURE: 11 0 0 0 0 0 0 0 0 0
ENERGY: 11 1734.6890 2134.2027 4545.0744 106.2239 -99999999999.9999 3539.0872 0.0000 0.0000 0.0000 -99999999999.9999 0.0000 -99999999999.9999 -99999999999.9999 0.0000

PRESSURE: 12 0 0 0 0 0 0 0 0 0
GPRESSURE: 12 0 0 0 0 0 0 0 0 0
ENERGY: 12 1708.7186 2183.8825 4547.4082 112.2657 -99999999999.9999 1619.1587 0.0000 0.0000 0.0000 -99999999999.9999 0.0000 -99999999999.9999 -99999999999.9999 0.0000

LINE MINIMIZER BRACKET: DX 4.20606e-05 4.20606e-05 DU -inf -nan DUDX -1.50758e+08 -6.15615e+07 -3.16109e+07
PRESSURE: 13 0 0 0 0 0 0 0 0 0
GPRESSURE: 13 0 0 0 0 0 0 0 0 0
ENERGY: 13 nan nan nan nan 0.0000 0.0000 0.0000 0.0000 0.0000 nan 0.0000 nan nan 0.0000