[phenixbb] simulated annealing

Pavel Afonine PAfonine at lbl.gov
Sat Jun 19 10:56:41 PDT 2010

Hi All,

from  what I see on this conversation for the last couple of days:

- I'm almost certain that there is something weird about the PDB file;

- I don't think that the high start SA temperature causes the problem. 
For some (unknown to me) reasons the SA code in PHENIX is very tolerant 
to super high start temperatures. At some point I tried 100000K or so 
and nothing bad happened.

If you really want us to debug this issue then the only way to do so is 
to send us enough of the inputs so we can reproduce this problems, 
explain what's happening and fix it.

Necessary inputs include:
- PDB file;
- data file;
- parameter file (if any);
- the command you used (and that results in problem).

Don't send these files to the whole phenixbb, but you can send them to 
my email directly and I will take care of it.

Also, it would be helpful if you explain what you are trying to achieve 
by running SA with such as hight start temperature. Just in case I might 
be able to suggest a better way of doing that...


On 6/19/10 10:38 AM, Nathaniel Echols wrote:
> On Sat, Jun 19, 2010 at 9:32 AM, jp d <yoyoq at yahoo.com 
> <mailto:yoyoq at yahoo.com>> wrote:
>     yes that temp is huge. my original error takes several hours to
>     get. so this test case is a much smaller pdb and mtz file.
>     at normal temp the error doesn't happen. but at high temp
>     it is the same behaviour as my large original data set.
> That doesn't tell us anything - the error could be caused by any 
> number of problems with the coordinates, and unless you're using 
> unrealistic high temperatures for the original data set too, there is 
> probably something else wrong with it.  In general you need to send us 
> the original data, parameter file, and log file if you want us to 
> debug problems like this (please use bugs at phenix-online.org 
> <mailto:bugs at phenix-online.org> or help at phenix-online.org 
> <mailto:help at phenix-online.org> for this, especially if it's 
> unpublished data).  However, after reading Ralf's reply, I'm not sure 
> if there is anything we can do if the problem is specific to simulated 
> annealing.
>     and at high temp it doesn't crash in 1.5 but does crash in 1.6
> This is a problem with version 1.5, not 1.6 - it should certainly not 
> continue to run if the protein bonds have been exploded.
> -Nat
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