vlimit exceeded for step 365; vmax = 228.6675
vlimit exceeded for step 366; vmax = 33.2803
This indicates that something is wrong with your simulation. There are large forces on some atoms that lead to large velocities. Possible reasons are a not well equlibrated system or problems with SCF convergence (often due to bad structures, lack of equilibration, or unsuitable choice of QM region).
ERROR: QM region + cutoff larger than box dimension:
QM-MM Cutoff = 5.0000
Your QM region is too large for the simulation box. The QM region plus QM/MM cutoff must fit into the simulation box. Either choose a smaller QM region or increase your simulation box size. A QM/MM cutoff of 5 Angstrom is quite small. You probably should increase it.
All the best,
Andy
—
Dr. Andreas W. Goetz
Associate Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu
Web: www.awgoetz.de
On Aug 5, 2024, at 9:15 AM, Kriti Shukla via AMBER <amber.ambermd.org> wrote:
Hey community,
I'm trying to do a QM/MM calculation with a QM region containing a residue
side chain towards the bulk. After running some initial simulations and
then propagating the run further using the previous restart file, I'm
encountering the following error:
```
NSTEP = 365 TIME(PS) = 6.365 TEMP(K) = 542.70 PRESS = 0.0
Etot = -430706.6989 EKtot = 81677.9591 EPtot = -512384.6580
BOND = 30546.9458 ANGLE = 4867.6533 DIHED = 2599.8929
1-4 NB = 1075.9879 1-4 EEL = 12497.3765 VDWAALS = 26450.2866
EELEC = -203658.8153 EHBOND = 0.0000 RESTRAINT = 0.0000
QUICKESCF= -386934.8552
CMAP = 170.8694
Ewald error estimate: 0.8459E-02
------------------------------------------------------------------------------
vlimit exceeded for step 365; vmax = 228.6675
vlimit exceeded for step 366; vmax = 33.2803
vlimit exceeded for step 367; vmax = 30.5074
vlimit exceeded for step 368; vmax = 27.7543
****************************************************
ERROR: QM region + cutoff larger than box dimension:
QM-MM Cutoff = 5.0000
Coord Lower Upper Size Radius of largest sphere inside unit cell
X -24.957 24.748 49.704 38.284
Y -38.553 38.242 76.795 38.284
Z -26.515 24.544 51.059 38.284
****************************************************
SANDER BOMB in subroutine QM_CHECK_PERIODIC<qm_mm.f>
QM region + cutoff larger than box
cannot continue, need larger box.
```
My protein is in a cubic box with dimensions of 15 angstroms. I also set
`iwrap=1`, but I'm still encountering the same error.
Does anyone have any suggestions for resolving this issue?
--
Kriti Shukla
Research Scholar
Department of Chemistry
Indian Institute of Technology, Kharagpur
India. 721302
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Received on Tue Aug 06 2024 - 00:00:02 PDT
