AMBER Archive (2003)

Subject: A problem in Sander production dynamics

From: yuann (yuann_at_bioinfo.ndhu.edu.tw)
Date: Mon Apr 14 2003 - 03:37:50 CDT

Dear AMBER users,

Recently I find there is something strange in my
production dynamics. I attempt to build a model of my
DNA and binding drugs, equlibrate them via NPT ensemble
step by step by gradually reducing the position restrain
from 100 to 0.2, and also energy minimization is applied
before these MD.

However, when I've run the production dynamics, the RMSd
result between the trajectories and the reference structure
(from PDB structure solved by NMR) shows a strange periodical
repeat every 120ps, and the repeat curves are almost the same.
I've tried even NPT or NVE ensemble on my production dynamics,
but the results are similar with this problem.

I run AMBER7 on AIX51 with 8cpu by MPI, and all bugfixs were applied
The following is my input for production dynamics, and a rmsd figure
is shown here http://bioinfo.ndhu.edu.tw/~yuann/TMP/sander7.gif

------
2ns Microcanonical MD(keep at 300K) T=245.000-2245.000

 &cntrl
   imin=0, dt=0.002, ntr=0, ntb=1, nstlim=1000000,
   irest=1, ntx=7, t=245.000,
   ntc=2, tol=0.0000001, ntf=1,
   ntt=0, vlimit=20.0,
   cut=10.0, nsnb=10,
   ntpr=50, ntwr=50, ntwx=50,
   nscm=2500, iwrap=1,
 &end
END

(ps. As to NPT ensemble is with ntb=2, TAUTP=5.0, NTP=1, TAUP=0.5) 

---

I've know ideas what does this result mean, or is this my problem
of MD strategy, or even the mistakes made by MPI parallel job?
Thanks for your ideas and suggestion.

Best Regards,

sychen.