Dear Amber Community,
I built an RNA system containing Mg2+ with a 12-6-4 LJ-type nonbonded model, which works well in cMD. However, when I use GaMD(igamd=1 or 2 or 3), I encountered an error message "of length = 42Failed an illegal memory access was encountered" while running pmemd.cuda, this occurred at the beginning of the equilibration. My input is as follows:
Equilibration stage (NPT)
&cntrl
imin = 0
irest = 1
ntx = 5
ntb = 2
iwrap = 1
ntt = 11
ig = -1
temp0 = 298.0
ntp = 1
barostat = 2
taup = 2.0
pres0 = 1.0
cut = 9.0
ntr = 0
ntc = 2
ntf = 2
nstlim = 26500000
dt = 0.0020
ntpr = 500
ntwx = 500
ntwr = 500000
ntwprt = 1024
ioutfm = 1
igamd = 3, iE = 1, irest_gamd = 0,
ntcmd = 1500000, nteb = 25000000, ntave = 100000,
ntcmdprep = 500000, ntebprep = 1000000,
sigma0P = 6.0, sigma0D = 6.0
/
Additionally, I made some attempts to figure out what was happening.
I tried running pmemd, and it worked well.
I attempted to use Mg2+ with a 12-6 LJ model, and pmemd.cuda ran successfully.
I tried running aMD, and when setting iamd=2 or 3, I encountered the same error "of length = 42Failed an illegal memory access was encountered." However, when setting iamd=1, it seemed to run fine.
Looking forward to any suggestions.
Best Regards,
Shen Yang
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Received on Mon Apr 15 2024 - 01:00:02 PDT
