Hi all,
I am simulating a small protein system with a Mg2+ GTP bound (Mg2+ params from frcmod.) I am using frcmod.ionslm_1264_tip3p for metal parameters and
http://www.pharmacy.manchester.ac.uk/bryce/amber/ for GTP parameters. I was able to generate prmtop and inpcrd for the system. However, I get this error message when running pmemd.cuda:
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
#0 0x7FEFF8B0C7D7
#1 0x7FEFF8B0CDDE
#2 0x7FEFF8247FEF
#3 0x46DB1A in __mol_list_mod_MOD_setup_molecule_lists
#4 0x4AE5F0 in __pme_alltasks_setup_mod_MOD_pme_alltasks_setup
#5 0x492034 in MAIN__ at pmemd.F90:?
/tmp/slurmd/job07160/slurm_script: line 27: 19155 Segmentation fault (core dumped)
The output file stops after line Energy averages sample interval:
| ene_avg_sampling = 1000
with no error message.
The md input file is:
&cntrl
imin = 0, nstlim = 100000, dt = 0.001,
irest = 0, ntx = 1, ig = 45678,
tempi = 100.0, temp0 = 298.0,
ntc = 2, ntf = 2, tol = 0.00001,
tautp = 0.1, taup = 0.1,
ntwx = 1000, ntwe = 0, ntwr = 1000, ntpr = 1000,
cut = 8.0, iwrap = 1,
ntt =1, ntb = 1, ntp = 0,
nscm = 0,
ntr=1, restraintmask="!:WAT & !.H=", restraint_wt=100.0
nmropt=1,
&end
&wt
TYPE="TEMP0", istep1=0, istep2=100000,
value1=100., value2=298.,
&end
&wt
TYPE="END",
&end
/
The system is able to minimize fine with pmemd. The same error occurs during MD when I run pmemd without cuda.
Thank you,
Ziheng Wang
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Received on Sat Aug 29 2015 - 01:30:03 PDT
