AMBER Archive (2006)

Subject: AMBER: Error in RST files in long simulations!

From: lucas luquitas (lucamaster_at_gmail.com)
Date: Mon Feb 20 2006 - 13:59:35 CST

Hi all,
 I am ruuning a normal constant temperature simulation of small protein(34aa) in
a periodic box of TIP3P waters. The simulation is quite long around
80ns, the problem
is when I want to restart the simulation, my restart file is corrupted!!
When I check, I see that some of the coordinates are above 1000, so it
prints ***********.
The other thing is that when I image and center and strip to view the
traj with VMD, I see jumping in the coordinates, like if it were
moving between boxes!

 Here is the inp file:
&cntrl
   imin=0,
   ntc=2, ntf=2,
   cut=12.0,
   ntpr=500, ntwx=10000, ntwv=10000,ntwe=500,
   nstlim=90000000, dt=0.002,
   ntt=1, tempi=300.0, temp0=300.0, tautp=1.0,
   ntx=5, irest=1, ntb=2,
   ntp=1, PRES0=1, TAUP=1,
   nscm=10000,
   ntr=0,
&end

Lucas
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