[gmx-users] Re: equilibrium stage runs for too long

[Dr. Vitaly Chaban]

> Dear Vitaly,
>
> here's the log file of the nvt simulation, and it was killed due to
> exceeding the wall time. Hopefully it could still provide some useful
> information. Thank you so much indeed!

>
> The initial number of communication pulses is: X 1 Y 1 Z 1
> The initial domain decomposition cell size is: X 1.33 nm Y 2.00 nm Z 8.00 nm
>
> The maximum allowed distance for charge groups involved in interactions is:
>                  non-bonded interactions           0.900 nm
>             two-body bonded interactions  (-rdd)   0.900 nm
>           multi-body bonded interactions  (-rdd)   0.900 nm
>   atoms separated by up to 5 constraints  (-rcon)  1.333 nm
>
> When dynamic load balancing gets turned on, these settings will change to:
> The maximum number of communication pulses is: X 1 Y 1 Z 1
> The minimum size for domain decomposition cells is 0.900 nm
> The requested allowed shrink of DD cells (option -dds) is: 0.80
> The allowed shrink of domain decomposition cells is: X 0.67 Y 0.45 Z 0.11
> The maximum allowed distance for charge groups involved in interactions is:
>                  non-bonded interactions           0.900 nm
>             two-body bonded interactions  (-rdd)   0.900 nm
>           multi-body bonded interactions  (-rdd)   0.900 nm
>   atoms separated by up to 5 constraints  (-rcon)  0.900 nm
>
>
> Making 3D domain decomposition grid 6 x 4 x 2, home cell index 0 0 0
> Center of mass motion removal mode is Linear
> We have the following groups for center of mass motion removal:
>   0:  rest
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> G. Bussi, D. Donadio and M. Parrinello
> Canonical sampling through velocity rescaling
> J. Chem. Phys. 126 (2007) pp. 014101
> -------- -------- --- Thank You --- -------- --------



Dear Clare -

So, we now see that the run freezes at its every beginning without
even writing the information for STEP 0.

Please, try to run your system using just one processor, i.e. no MPI
in the invocation like (or maybe even faster, using a command line and
see what the MDRUN says).

Cheers,

Dr. Vitaly V. Chaban, 430 Hutchison Hall
Dept. Chemistry, University of Rochester
120 Trustee Road, Rochester, NY 14627-0216
THE UNITED STATES OF AMERICA