[gmx-users] Performance

[M.Naser]

Hi Anton,

Thanks for your very informative reply. What sort of contraint is normally
used?

With regards,

Abu

> M.Naser wrote:
>
>> Hi All,
>>
>> Is there any trick for improving the performance of a lam/mpi parallel
>> run?
>
> No, except waiting for the next version which should have a completely
> overhauled parallelization scheme.
>
>> I am aware of the flags : sort. shuffle and load.
>
> You write full precision out coordinates, velocities and forces
> (nstxout, nstvout, nstfout) every 100 steps (0.1 with your 1 fs
> timestep). It may be that writing this amount of data to disk is the
> limiting step in your case, and in any case it seems you are wasting
> disk-space (although that may not be a problem for you...).
>
> In general, full precision x and v are required only for making
> re-starts, for nearly all analysis purposes, the reduced precision
> coordinates (nstxtcout) will be good enough!
>
> Most people use a 2 fs timestep and constraints (like David suggested),
> and set nstxout and nstvout to something like 10000; nstfout you can set
> to zero.
>
>
> --
> Groetjes,
>
> Anton
>
> * NOTE: New Phone & Fax numbers (below) *
>
>   _____________ _______________________________________________________
> |             |                                                       |
> |  _   _  ___,| K. Anton Feenstra                                     |
> | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
> |(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
> | \_/ \_/ | | | Tel: +31 20 59 87608 - Fax: +31 20 59 87610           |
> |             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
> |             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
> |_____________|_______________________________________________________|
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>



__________________________________________________________________

DISCLAIMER:

This e-mail message is subject to http://www.hw.ac.uk/disclaim.htm
__________________________________________________________________