AMBER: the problem of mdcrd

From: xiphias xie <xiphiasxp.yahoo.com.cn>
Date: Mon, 16 Jan 2006 17:16:09 +0800 (CST)

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



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Received on Tue Jan 17 2006 - 06:10:05 PST
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