On Mon, Jun 28, 2010 at 2:40 AM, Homa Azizian <homa.azizian.anu.edu.au>wrote:
> I have done simulation for 200 ps and save the trajectory file every 500
> step, so I save every 1 ps in the out put trajectory and I have 200 frams,
> Is it correct?
>
Yes, it's correct.
> mdin file:
> imin = 0, irest = 1, ntx = 5,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 10, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 298.0, temp0 = 298.0,
> ntt = 1, gamma_ln = 0,
> nstlim = 100000, dt = 0.002,
> ntpr = 100, ntwx = 500, ntwr = 1000
> Now for analysing I want to reduce the frame, insted of using all the 200
> frames using 20 frames ( 1/10 ) in 200 ps. how can I do it? can I do it by
> this command?
> trajin *.mdcrd.gz 1 200 10
>
In ptraj, yes.
> by the above command the total 200 ps simulation is reduced to 20 ps. (from
> checking the rmsf result insted of having 200 ps I have 20 ps).
>
No, it is still 200 ps. You're just using fewer snapshots. I suppose if
you wanted to be strictly correct, it would be just under 200 ps, since the
above command will used frames 1, 11, 21, ..., 191 (20 frames total).
Therefore, you'll be using apparently 191 ps. If you want to use frames 10,
20, 30, 40, ..., 200, you have to change the above to
trajin *.mdcrd 10 200 10
It's an important distinction, because 20 frames spaced over a 200 ps
trajectory will give a lot more fluctuation than 20 frames spaced over a 200
fs trajectory.
>
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Jun 28 2010 - 05:00:05 PDT
