Hi David,
I was trying to upload some of my files. But once I sent out, I receive
message from amber-bounces telling me that message body is too big and need
to be reviewed by list moderator... Can you see my previous posts? Any
other way I can show you my .nab, .job, .prmtop, .pdb, and .out files...?
Thank you very much!
Guqin
2014-05-28 9:39 GMT-04:00 David A Case <case.biomaps.rutgers.edu>:
> On Tue, May 27, 2014, Guqin Shi wrote:
> > >
> > > 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.......
>
> I've never seen this behavior. [It is still unclear to me what you mean by
> the term "forever", but I'll assume(?) you mean some very large value. You
> have about 5,000 degrees of freedom, so it make take much longer than 5,000
> steps to achieve convergence.]
>
> Could you provide a prmtop file and one frame
> that is giving you problems (along with the nab code you are using)? I
> didn't
> see anything in the code you provided that would make the forces and energy
> incompatible (the usual cause of minimization failures), but maybe I missed
> something.
>
> ...dac
>
>
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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 Wed May 28 2014 - 14:30:02 PDT
