# RE: AMBER: (no subject)

From: Ross Walker <ross.rosswalker.co.uk>
Date: Sat, 4 Aug 2007 08:30:36 -0700

Hi Syed,

This is basic mathematics.

1) Step 1 - determine how many ps your run corresponds to. This is timestep
in ps * nstlim. So dt*nstlim. If you did 2500 steps with dt=0.002 (2fs) then
your run corresponds to 5ps. (we will call this value x)

2) Work out how many seconds it took to run. Check then end of the output
file where it conveniently tells you. (We will call this value t) E.g.
150.0s

3) To get ps per day we first have to work out how many lots of x could be
done in a day. There are 86400 seconds in a day (60x60x24) and we know it
takes t seconds to do one lot of x. So in 1 day we get 86400/t lots of x
completed.(Call this value y) E.g. 86400/150.0 = 576

4) Now we know how many lots of x we can get done in a day (y) so to get ps
per day we multiply y by the number of ps that x represents. So 576 x 5 =
2880 ps per day (or 2.88 ns/day).

Short version:

86400 * dt * nstlim
---------------------------
time

I am amazed you couldn't work that out for yourself.

Good luck.

Ross

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From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Syed Tarique Moin
Sent: Saturday, August 04, 2007 07:07
To: amber.scripps.edu
Subject: Re: AMBER: (no subject)

I have the program xmgrace to draw a graph, so suggest me to calcute the ps
/ day.

Now i can understand that what i have to do. can i extract or find out
information about ps/day from the output file of sander.

Regards

Carlos Simmerling <carlos.simmerling.gmail.com> wrote:

do you have a program to make graphs?
if yes, then you should run a short test with different
number of processors. convert the run time to
ps/day as we explained before. do this for different #
processors and make a table, then plot it.
You'll have to be more specific about which step is confusing.

On 8/4/07, Syed Tarique Moin wrote:
> Hello
>
> Yeah ! The same thing i want to to do i.e. ps/day vs number of processors
in
> the form of graphical representation.
>
> Regards
>
> Gustavo Seabra wrote:
>
> I'm nut sure I understand what you mean, but I'd think you want to do a
plot
> with "ps/day vs. number of processors" , no? ps/day alone will not give
you
> anything to plot.
>
> Gustavo.
>
>
>
> ________________________________
> From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
Of
> Syed Tarique Moin
> Sent: Thursday, August 02, 2007 8:36 AM
> To: amber.scripps.edu
> Subject: Re: AMBER: (no subject)
>
>
>
> Hello,
>
> Yeah! but i want to know how to manipulate these in graphical
representation
> as ps/day.
>
> Kindly guide me
>
>
> Syed Tarique Moin,
> Junior Research Fellow,
> H.E.J. Research Institute of Chemistry,
> International Center for Chemical and Biological Sciences,
> University of Karachi, Karachi-75720, Pakistan
>
> tarisyed.yahoo.com
> tarisyed.hotmail.com
>
> ________________________________
> Park yourself in front of a world of choices in alternative vehicles.
> Visit the Yahoo! Auto Green Center.
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Syed Tarique Moin,
Junior Research Fellow,
H.E.J. Research Institute of Chemistry,
International Center for Chemical and Biological Sciences,
University of Karachi, Karachi-75720, Pakistan

tarisyed.yahoo.com
tarisyed.hotmail.com

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