From: Ale Gomez (agomez_at_physics.org)
Date: Sun Nov 08 2009 - 11:19:28 CST
Hi Roman and thanks for your advice.
I have tried disassembling my system before and seems like it works. I
hadn't finish it yet but I wanted just one script or one procedure to do it.
Maybe I should do it in that way.
My original conf file is this:
*############################################################
## JOB DESCRIPTION ##
#############################################################
# Minimization of neutral
# Bacteriorhodopsin in a neutral lipid membrane
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure bacrhodopsin_final.psf
coordinates bacrhodopsin_final.pdb
outputName bacrhodop_min
set temperature 0
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters par_all27_prot_lipidNBFIX.prm
temperature 0
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 8.
pairlistdist 13.5
# Integrator Parameters
timestep 1.0 ;# 1fs/step
rigidBonds all ;# needed for 1fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20
# Output
restartfreq 1000 ;# 1000steps = every 2ps
dcdfreq 1000
xstFreq 1000
outputEnergies 50
outputPressure 50
#############################################################
## EXTRA PARAMETERS ##
#############################################################
# Periodic Boundary Conditions
# NOTE: Do not set the periodic cell basis if you have also
# specified an .xsc restart file!
if {1} {
cellBasisVector1 82. 0. 0.
cellBasisVector2 0. 79. 0.
cellBasisVector3 0. 0. 65.98
cellOrigin -0.05074617639183998 0.1211656779050827
1.0147390365600586
}
wrapWater on
wrapAll on
#PME (for full-system periodic electrostatics)
if {1} {
PME yes
PMEGridSizeX 80
PMEGridSizeY 80
PMEGridSizeZ 90
}
}
############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 10000
*
As you can see I tried to minimize in 10000 steps and setup the energy
output in 50, but it doesn't work.
Just one more question, how can I now if there is some atoms overlapped in
my system??. I followed the procedure of the Membrane NAMD Tutorial to
prepare my system.
Thanks for all your help.
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 Roman Petrenko <rpetrenko_at_gmail.com>
> 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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