[phenixbb] geometry

[Jianghai Zhu]

You are right.  After more cycles, the geometry seems to be normal now.  I am a little surprised that it didn't converge since I have actually refined it many cycles before.  But then again, I did some major rebuilding before this round.

-- Jianghai




On Nov 9, 2010, at 11:31 AM, Pavel Afonine wrote:

> Hi Jianghai,
> 
> what I see looking at this bunch of numbers is that they are still changing with the macro-cycle number, telling me that the refinement is not converged yet. So I suggest to do more macro-cycles and see what happens. If after that you will still be puzzled then I would need to look at the input files that you used for refinement to say something more useful.
> 
> Pavel.
> 
>> Hi all,
>> 
>> I am refining a 2.75 A structure.  The wxc_scale is 0.02, optimize_wxc is false. But the geometry I got doesn't make sense at all.  Any explanations?
>> 
>> ------------------------------------------------------------------------
>>  stage       angl   bond   chir   dihe   plan   repu  geom_target
>>    0    :   0.617  0.004  0.039 14.275  0.003  4.123   5.8886e-02
>>    1_bss:   0.617  0.004  0.039 14.275  0.003  4.123   5.8886e-02
>>    1_xyz:   3.391  0.059  0.209 16.068  0.010  4.114   1.3055e+00
>>    1_adp:   3.391  0.059  0.209 16.068  0.010  4.114   1.3055e+00
>>    2_bss:   3.391  0.059  0.209 16.068  0.010  4.114   1.3055e+00
>>    2_xyz:   2.435  0.032  0.180 15.961  0.007  4.114   5.4206e-01
>>    2_adp:   2.435  0.032  0.180 15.961  0.007  4.114   5.4206e-01
>>    3_bss:   2.435  0.032  0.180 15.961  0.007  4.114   5.4206e-01
>>    3_xyz:   2.139  0.025  0.191 15.477  0.007  4.114   3.7907e-01
>>    3_adp:   2.139  0.025  0.191 15.477  0.007  4.114   3.7907e-01
>> ------------------------------------------------------------------------
>> 
>> Thanks.
>> 
>> 
>> -- Jianghai
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