Re: Error in Minimization

From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Sun Nov 08 2009 - 10:29:47 CST

Hello Ale,
looks like you have atom overlaps in your system. Look in namd
tutorial about energy output lines!

ENERGY: 77 118703.4864 13094.4375 5678.0420
2300.9903 456312.2570 9999999999.9999 0.0000
0.0000 0.0000 9999999999.9999 0.0000
9999999999.9999 9999999999.9999 0.0000 66304287.8116
51466333.5562 427418.4400 66304287.8116 51466333.5562

If increasing the number of minimization steps to something like 500
or 1000 doesn't help, you should more carefully look at the system you
setup. Maybe, disassembling the system is required, so that you first
minimize protein, then minimize protein+lipids, and so on...

Any system with "infinite energy" (9999999999.9999) is going to crash namd.

On Sun, Nov 8, 2009 at 10:15 AM, Ale Gomez <agomez_at_physics.org> wrote:
> Hi Josh...
> Thanks for your answer. I want to study the behavior of bacteriorhodopsin in
> a lipid membrane. First I prepared my system: put the protein in a solvate,
> then in the lipid membrane and then remove extra atoms. I think that my
> prepared system is ok (probably not, that's the reason I attached the tcl
> script that I made). With my complete system I want to minimize it, then
> warm it up to 300 degrees and then try to equilibrate the system.
> When I ran the NAMD minimize script seems to be ok, but when it is finish I
> look into the log file and the values never change. It seems like that:
>
> LINE MINIMIZER BRACKET: DX 0 2.60819e-27 DU 0 0 DUDX -4.50299e+14
> -4.50299e+14 -4.50299e+14
> PRESSURE: 75 6.36711e+07 -195549 -1.28311e+06 -195549 6.28248e+07 -488651
> -1.28311e+06 -488651 7.24169e+07
> GPRESSURE: 75 4.91079e+07 -228040 -1.75324e+06 -225861 4.83403e+07 -447628
> -1.74294e+06 -588612 5.69508e+07
> ENERGY:      75    118703.4864     13094.4375      5678.0420
> 2300.9903         456312.2570 9999999999.9999         0.0000
> 0.0000         0.0000      9999999999.9999         0.0000 9999999999.9999
> 9999999999.9999         0.0000       66304287.8116  51466333.5562
> 427418.4400  66304287.8116  51466333.5562
>
> LINE MINIMIZER BRACKET: DX 1.30409e-27 1.30409e-27 DU 0 0 DUDX -4.50299e+14
> -4.50299e+14 -4.50299e+14
> LINE MINIMIZER REDUCING GRADIENT FROM 5.40359e+14 TO 5.40359e+11
> PRESSURE: 76 6.36711e+07 -195549 -1.28311e+06 -195549 6.28248e+07 -488651
> -1.28311e+06 -488651 7.24169e+07
> GPRESSURE: 76 4.91079e+07 -228040 -1.75324e+06 -225861 4.83403e+07 -447628
> -1.74294e+06 -588612 5.69508e+07
> ENERGY:      76    118703.4864     13094.4375      5678.0420
> 2300.9903         456312.2570 9999999999.9999         0.0000
> 0.0000         0.0000      9999999999.9999         0.0000 9999999999.9999
> 9999999999.9999         0.0000       66304287.8116  51466333.5562
> 427418.4400  66304287.8116  51466333.5562
>
> LINE MINIMIZER BRACKET: DX 0 5.49628e-28 DU 0 0 DUDX -5.40359e+14
> -5.40359e+14 -5.40359e+14
> PRESSURE: 77 6.36711e+07 -195549 -1.28311e+06 -195549 6.28248e+07 -488651
> -1.28311e+06 -488651 7.24169e+07
> GPRESSURE: 77 4.91079e+07 -228040 -1.75324e+06 -225861 4.83403e+07 -447628
> -1.74294e+06 -588612 5.69508e+07
> ENERGY:      77    118703.4864     13094.4375      5678.0420
> 2300.9903         456312.2570 9999999999.9999         0.0000
> 0.0000         0.0000      9999999999.9999         0.0000 9999999999.9999
> 9999999999.9999         0.0000       66304287.8116  51466333.5562
> 427418.4400  66304287.8116  51466333.5562
>
> It seems like nothing change and in my opinion must change, am I right???.
> Probably I am making something wrong but I spent a lot of time trying to fix
> it but nothing happend. What you think??
> Regards
>
> -------------------------------------------------------------------
> Ale Gomez
> Biophysics and Molecular Modelling Group
> Physics Department
> Escuela Politecnica Nacional, Quito-Ecuador
> Ladron de Guevara E11-253.
> Phone: 593-95292408
> http://www.ciencias.epn.edu.ec/~biomod/
>
>
> 2009/11/8 Joshua Adelman <jadelman_at_berkeley.edu>
>>
>> Hi Ale,
>> It is unclear from your email what the problem is you are attempting to
>> describe. You need to provide more detail into what you saw and what you
>> expected to see that makes you think the result is incorrect.
>> Best wishes,
>> Josh
>> On Nov 7, 2009, at 11:45 AM, Ale Gomez wrote:
>>
>> Hi everyone.
>> I try to minimize a protein, bacrhodopsin, in a lipid membrane. But
>> everything looks great until minimize is ready. When I saw the log file
>> seems that anything had change. Could anybody help me.
>> I attached preparation script for vmd (preparacion.tcl) and minimize
>> script for namd (bacmin.conf).
>> Regards
>>
>> -------------------------------------------------------------------
>> Ale Gomez
>> Biophysics and Molecular Modelling Group
>> Physics Department
>> Escuela Politecnica Nacional, Quito-Ecuador
>> Ladron de Guevara E11-253.
>> Phone: 593-95292408
>> http://www.ciencias.epn.edu.ec/~biomod/
>> <preparacion.tcl><bacmin.conf>
>
>
>

-- 
Roman Petrenko
Physics Department
University of Cincinnati

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