2014-05-27 20:25 GMT-04:00 David A Case <case.biomaps.rutgers.edu>:
> On Tue, May 27, 2014, Guqin Shi wrote:
> >
> > So my question is, here, readparm() can assure that my minimization step
> > takes disulfide bond into account, right?
>
> Yes.
>
> >
> >
> > My second problem is:
> > Is it common that minimization get stuck at some level of rmsg...?
> >
> > Here in the script, I set rmsg to 10^-4 and used XMIN method 3.
> > 624 frames out of 2000 got stuck, which means they can never descend
> below
> > 10^-4.
>
> How bit is your system? Have you run more than 5000 steps?
>
> ....dac
>
> There are 1568 atoms in my system (99 residues). Usually it stuck at one
> rms forever. I did elongate steps for some frames. And it keeps
> stucking.......
>
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--
Guqin SHI
The Ohio State University
College of Pharmacy
500 W. 12th Ave.
Columbus, OH, 43210
(614)688-3531
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Received on Tue May 27 2014 - 20:00:03 PDT
