Hi David,
The box size is here:
Solute vdw bounding box: 135.504 120.504 95.504
Total bounding box for atom centers: 162.904 147.904 122.904
Solvent unit box: 18.865 18.478 19.006
Total vdw box size: 166.143 150.883 125.535 angstroms.
Volume: 3146931.024 A^3
Total mass 1729772.416 amu, Density 0.913 g/cc
1. Checking parameters for unit 'bic'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 1
Unit is OK.
Checking parameters for unit 'prot'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 1
Unit is OK.
2. I can make it through two short rounds of minimization, using a couple
hundred cycles total. The final energy is pretty low:
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
80 -1.0728E+06 2.1341E+01 1.0576E+04 O2 6984
BOND = 589516.2494 ANGLE = 4608.9671 DIHED =
3317.8961
VDWAALS = 174751.9838 EEL = -1839252.0573 HBOND =
0.0000
1-4 VDW = 1490.7925 1-4 EEL = -7562.9974 RESTRAINT =
0.0000
CMAP = 350.6766
However, this crashes immediately upon starting heating.
Best,
Christian
On Tue, Aug 23, 2022 at 5:12 AM David A Case <david.case.rutgers.edu> wrote:
> On Tue, Aug 23, 2022, Christian Seitz via AMBER wrote:
> >
> >I have run a short minimization on a system, and am trying to run the
> >heating for it. When I do this, I get this error before any cycles are
> >finished:
> >
> >Error: an illegal memory access was encountered launching kernel
> kNLSkinTest
>
> What is the box size in your system? Also, the following:
>
> 1. use the checkstructure action in cpptraj to make sure you don't have any
> bad bonds or contacts.
>
> 2. Run a short simulation on the CPU, with ntpr=1. Make sure the starting
> energy is very close to the final energy from minimization. Look for
> any problems that might arise.
>
> ....good luck...dac
>
>
--
*Christian Seitz*
PhD Candidate, Biochemistry & Biophysics | UC-San Diego
NSF GRFP Fellow, Amgen Scholar
McCammon lab <https://mccammon.ucsd.edu/> and Amaro lab
<https://amarolab.ucsd.edu/>
cseitz.ucsd.edu <cseitz.elon.edu>
[image: www.linkedin.com/in/christianseitz21]
<http://www.linkedin.com/in/christianseitz21>
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Received on Wed Aug 31 2022 - 11:00:24 PDT
