Dear experts,
I am currently performing umbrella sampling on a protein-ligand system,
where I defined the CV as the intramolecular distance between two atoms
within the inhibitor molecule. However, during the simulation runs, I
encountered a persistent issue: the output energy values appear as
asterisks ("*****"), indicating numerical instability or a crash.
Additionally, the velocity limit is exceeded at multiple steps.
To troubleshoot, I attempted simulations using various force constants (5,
10, 15, and 20 kcal/mol/Ų), but the problem persisted across all these
values. I also tested the runs using both sander.MPI and pmemd, but the
results remained the same.
Upon visual inspection of the trajectories, I observed that the system
becomes highly distorted or disrupted during the simulation. It seems the
restraint or initial configuration might be causing instability, but I am
unsure of the exact cause. Please help me out with this.
Thank you.
*Outputfile:*
APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.33
| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.80
|---------------------------------------------------
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
Etot = ************** EKtot = 0.0000 EPtot =
**************
BOND = 22150.0475 ANGLE = 1030.2486 DIHED =
812.2133
UB = 0.0000 IMP = 0.0000 CMAP =
81.1829
1-4 NB = 419.7488 1-4 EEL = 3333.8362 VDWAALS =
**************
EELEC = -155305.2758 EHBOND = 0.0000 RESTRAINT =
2.1654
EAMBER (non-restraint) = **************
Ewald error estimate: 0.2035E-04
------------------------------------------------------------------------------
NMR restraints: Bond = 2.165 Angle = 0.000 Torsion = 0.000
===============================================================================
vlimit exceeded for step 0; vmax = **********
vlimit exceeded for step 1; vmax = **********
vlimit exceeded for step 2; vmax = 24164.8026
vlimit exceeded for step 3; vmax = 77086.3499
vlimit exceeded for step 4; vmax = 2401.3186
vlimit exceeded for step 5; vmax = 6637.0897
vlimit exceeded for step 6; vmax = **********
vlimit exceeded for step 7; vmax = 15624.3374
*Input file:*
&cntrl
imin=0,
nstlim=2000000,
dt=0.001,
temp0=300.0,
ntpr=1000,
ntwx=1000,
cut=10.0,
ntb=1,
ntp=0,
ntt=3,
gamma_ln=2.0,
*irest=0, ntx=1,*
iwrap=1,
nmropt=1,
/
&end
&wt
type='DUMPFREQ', istep1=10,
&end
&wt
type='END',
&end
DISANG=win1.in
DUMPAVE=distance1.dat
*Win.in:*
Harmonic restraints
&rst
iat=1895,1867,
r1=2.5, r2=3, r3=3, r4=3.5,
rk2=10.0, rk3=10.0,
/
------------------------------
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Received on Sat Aug 02 2025 - 00:30:02 PDT
