Hello,
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
My heating input file looks like this:
Heat
&cntrl
imin=0,
ntx=1,
irest=0,
nstlim=500000,
dt=0.002,
ntf=2,
ntc=2,
tempi=10.0,
temp0=300.0,
ntpr=1000,
ntwx=1000,
cut=8.0,
ntb=1,
ntp=0,
ntt=3,
gamma_ln=5.0,
nmropt=1,
ig=-1,
restraint_wt=1.0,
restraintmask='.CA,C,O,N&!:WAT'
/
&wt type='TEMP0', istep1=0, istep2=2000000, value1=10.0, value2=300.0 /
&wt type='TEMP0', istep1=2000001, istep2=5000000, value1=300.0,
value2=300.0 /
&wt type='END' /
I have seen this error when using amber 18, amber 20 and amber 22. I have
also seen it for the ff14sb and ff19sb force fields. I do not have any
ligands present in my system, which appeared to be the culprit for someone
previously (
http://archive.ambermd.org/202011/0195.html), though I do have
dozens of bicarbonate ions that I have added to my solvent. Additionally,
my restraint weight is not too high as was also seen previously (
http://archive.ambermd.org/202110/0250.html). What might be the issue?
Thanks in advance!
Best,
Christian
--
*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 Tue Aug 23 2022 - 00:30:03 PDT
