AMBER Archive (2003)

Subject: Re: A problem in Sander production dynamics

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Mon Apr 14 2003 - 06:21:04 CDT

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
===================================================================
Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

----- Original Message -----
From: "yuann" <yuann_at_bioinfo.ndhu.edu.tw>
To: <amber_at_heimdal.compchem.ucsf.edu>
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 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.
>
>