Re: A problem in Sander production dynamics

From: Carlos Simmerling <>
Date: Mon, 14 Apr 2003 07:21:04 -0400

have you looked at the dynamics visually?
I think it is unlikely you go up to 16A RMSD
and then back to 2- that is a large drop. See
what the 16A looks like, it is bending? or imaging
in the box and you don't re-image the strands
before RMSD calculation? calculate the RMSD for
each strand, and then with/without the drug.
you may need to use ptraj to image.
I find it always helps to look at a movie
before carrying out any detailed analysis.
otherwise check your RMSD calculation, you
didn't tell us how or which atoms or what was
fit, etc.
Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web:
Stony Brook, NY 11794-5115 E-mail:

----- Original Message -----
From: "yuann" <>
To: <>
Sent: Monday, April 14, 2003 4:37 AM
Subject: A problem in Sander production dynamics

> 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
> ------
> 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
> (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.
Received on Mon Apr 14 2003 - 12:53:01 PDT
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