Re: AMBER: the problem of mdcrd

From: Vlad Cojocaru <Vlad.Cojocaru.eml-r.villa-bosch.de>
Date: Mon, 16 Jan 2006 10:55:45 +0100

what I don't really understand from your script is why the initial
temperature (tempi) is 356 while the temperature that you want to keep
your system (temp0)is 300 ....

vlad

xiphias xie wrote:

>Dear Amberers:
>
> I encountered a strange problem in running MD
>Equilibration on the whole system . My job is normaly
>ended ,the .out file is complete.but when i see the
>.mdcrd file by using VMD ,it just display a part of
>the trajectiory. when i run ptraj to calculate the
>RMSD,it displays that:
>
>ERROR in readAmberTrajectory(): Set #48 has coordinate
>out of bounds (i.e. *****'s)
>PTRAJ: Successfully read in 47 sets and processed 47
>sets.
>the total sets is not 47 sets ,but 1000 sets .
>here is my .in file:
>&cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 10, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 356.65, temp0 = 300.0,
> ntt = 1,
> nstlim = 250000, dt = 0.002,
> ntpr = 250, ntwx = 250, ntwr = 1000
> /
>I repeated it 3 times ,i encountered this every time
>.
>Could you please give me a suggestion?
>
>Thank you very much in advance !
> xiphias
>
>
>
>__________________________________________________
>ϿעŻ?
>http://cn.mail.yahoo.com
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-- 
Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298
e-mail: Vlad.Cojocaru.eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/
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Received on Tue Jan 17 2006 - 06:10:05 PST
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