Dear users and developers
I am trying to calculate the free energy of calcium binding to protein
using Amber20, then got errors like
*** Error in `pmemd.cuda': corrupted size vs. prev_size: 0x000000000a19c100
***
======= Backtrace: =========
/lib64/libc.so.6(+0x7f474)[0x7f21667ab474]
/lib64/libc.so.6(+0x8156b)[0x7f21667ad56b]
pmemd.cuda(__ti_mod_MOD_ti_cleanup+0xa1)[0x55a3a1]
pmemd.cuda(__runmd_mod_MOD_runmd+0x8389)[0x4e2259]
pmemd.cuda[0x522406]
pmemd.cuda(main+0x1d)[0x45946d]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f216674e555]
pmemd.cuda[0x46d6d7]
======= Memory map: ========
00400000-05690000 r-xp 00000000 fd:00 101359597
/usr/share/AMBER/amber20_src/bin/pmemd.cuda_SPFP
0588f000-05890000 r--p 0528f000 fd:00 101359597
/usr/share/AMBER/amber20_src/bin/pmemd.cuda_SPFP
05890000-05894000 rw-p 05290000 fd:00 101359597
/usr/share/AMBER/amber20_src/bin/pmemd.cuda_SPFP
05894000-05c7e000 rw-p 00000000 00:00 0
06b21000-140a2000 rw-p 00000000 00:00 0
[heap]
200000000-200200000 rw-s 00000000 00:05 32835
/dev/nvidiactl
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
One of the input files is as follows
TI simulation
&cntrl
imin = 0, nstlim = 100000, irest = 1, ntx = 5, dt = 0.002,
ntt = 3, temp0 = 300.0, gamma_ln = 2.0, ig = -1,
ntc = 2, ntf = 1,
ntb = 2,
ntp = 1, pres0 = 1.0, taup = 2.0,
ioutfm = 1, iwrap = 1,
ntwe = 100, ntwx = 100, ntpr = 100, ntwr = 200,
icfe = 1, clambda = 0.7, scalpha = 0.5, scbeta = 12.0,
logdvdl = 1,
mbar_states = 11
mbar_lambda = 0.00, 0.10, 0.20, 0.30, 0.40, 0.50, 0.60, 0.70, 0.80,
0.90, 1.00,
mcwat=1, mcrescyc=10000, mcint=1000
mcresstr='WAT'
ifsc=1, timask1='', timask2=':1', crgmask=':1', scmask1='', scmask2 =
':1'
/
&ewald
/
There is no issue if run without MC. Where maybe the problem and how can I
fix it?
Sincerely
Abdul Basit
Research Fellow
School of Computational & Integrative Sciences
Jawaharlal Nehru University, New Delhi-110067
India
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Received on Sat Jul 10 2021 - 23:00:03 PDT
