> NetCDF error: Permission denied
Is mdout being written successfully to the same directory?
Bill
On 5/24/17 8:28 PM, Neha Gandhi wrote:
> 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
>
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Received on Wed May 24 2017 - 21:30:03 PDT
