Hi List,
I am trying to perform production runs using GaMD. I get this error in the
output file
wrapping first mol.: 24.77751 35.04069 60.69226
NetCDF error: Permission denied
write_nc_restart(): Could not open restart
My input file is as below
&cntrl
imin = 0, irest = 1, ntx = 5,
nstlim = 25000000, dt = 0.002,
ntc=2,ntf=2,ig=-1,iwrap=1,
cut=12.0, ntb=2, ntp=1, taup=2.0,
ntpr=2500, ntwx=2500, ntwr=2500,
ntt=3, gamma_ln=3.0,
temp0=293.0,
igamd = 3, iE = 1, irest_gamd = 0,
ntcmd = 0, nteb = 0, ntave = 167724,
ntcmdprep=0, ntebprep=0,
sigma0P = 6.0, sigma0D = 6.0,
&end
I have total 4 simulations with different peptide and I use similar input
files for the job using pmemd.cuda. 3 out of 4 simulations crashes with
above error whereas simulation 1 is still ongoing. I tried running crashed
simulations on other machine with gpu node, they work fine.
Regards,
Neha
--
Regards,
Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Australia
LinkedIn
Research Gate
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 24 2017 - 20:30:03 PDT
