From: Ale Gomez (agomez_at_physics.org)
Date: Sun Nov 08 2009 - 09:15:02 CST
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*
2009/11/8 Joshua Adelman <jadelman_at_berkeley.edu>
Hi Ale,
This archive was generated by hypermail 2.1.6
: Wed Feb 29 2012 - 15:53:28 CST
*
-------------------------------------------------------------------
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/
>
> 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>
>
>
>