[gmx-users] energy minimization

[Justin Lemkul]

On 1/6/18 10:10 AM, rose rahmani wrote:
> Hi,
>
> I want to calculate the number of density profile of water.the initial .gro
> file which i have,has amino acid in itself, which should not be present in
> this analyze. So, i had to remove amino acid, and then, when i wanted to do
> energy minimization again, it's crushed and gave me step files.
> maybe it's because of modifying the initial gro file but i didn't have any
> choice i think so! because i have another structures in initial.gro file
> which i don't want to modify their coordinates.and all structure are in the
> center of box and the rest of the box should be empty.
> would you please help me? what is the alternative?

Why do you have to remove the amino acid to do this analysis? You're 
creating a rather large void, which will make nearby waters unstable. In 
the analysis, you're going to have a volume occupied by the amino acid 
that yields zero water density. That's going to happen irrespective of 
whether or not you remove the amino acid, so save yourself some trouble 
and don't mess with the coordinates.

-Justin

> with regards
>
>
>
>
> this is em.job
>
> Steepest Descents:
>     Tolerance (Fmax)   =  1.00000e+01
>     Number of steps    =         5000
> Step=    0, Dmax= 1.0e-02 nm, Epot= -6.05768e+04 Fmax= 1.07096e+04, atom=
> 815
> Step=    1, Dmax= 1.0e-02 nm, Epot= -6.12124e+04 Fmax= 5.57695e+03, atom=
> 4307
> Step=    2, Dmax= 1.2e-02 nm, Epot= -6.20952e+04 Fmax= 3.16416e+03, atom=
> 4307
> Step=    3, Dmax= 1.4e-02 nm, Epot= -6.33594e+04 Fmax= 1.87516e+03, atom=
> 4302
> Step=    4, Dmax= 1.7e-02 nm, Epot= -6.50390e+04 Fmax= 1.68178e+03, atom=
> 4303
> Step=    5, Dmax= 2.1e-02 nm, Epot= -6.64168e+04 Fmax= 1.54347e+03, atom=
> 4303
> Step=    6, Dmax= 2.5e-02 nm, Epot= -6.76032e+04 Fmax= 1.08368e+03, atom=
> 4303
> Step=    7, Dmax= 3.0e-02 nm, Epot= -6.89478e+04 Fmax= 1.16283e+03, atom=
> 4303
> Step=    8, Dmax= 3.6e-02 nm, Epot= -6.98965e+04 Fmax= 9.72829e+02, atom=
> 4303
> Step=    9, Dmax= 4.3e-02 nm, Epot= -7.08234e+04 Fmax= 8.39105e+02, atom=
> 4303
> Step=   10, Dmax= 5.2e-02 nm, Epot= -7.14550e+04 Fmax= 5.18546e+03, atom=
> 4302
> Step=   11, Dmax= 6.2e-02 nm, Epot= -7.17534e+04 Fmax= 8.04910e+02, atom=
> 4302
> Step=   12, Dmax= 7.4e-02 nm, Epot= -7.22134e+04 Fmax= 1.00656e+04, atom=
> 4301
> Step=   13, Dmax= 8.9e-02 nm, Epot= -7.25685e+04 Fmax= 1.07787e+03, atom=
> 4303
>
> step 14: Water molecule starting at atom 2018 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> step 14: Water molecule starting at atom 1265 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
> Step=   14, Dmax= 1.1e-01 nm, Epot=  2.77257e+05 Fmax= 2.29207e+09, atom=
> 2018^M
> step 15: Water molecule starting at atom 1331 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
> Step=   15, Dmax= 5.3e-02 nm, Epot= -7.20611e+04 Fmax= 1.56839e+06, atom=
> 1331^MStep=   16, Dmax= 2.7e-02 nm, Epot= -7.28049e+04 Fmax= 4.98605e+02,
> atom= 4301
> Step=   17, Dmax= 3.2e-02 nm, Epot= -7.31402e+04 Fmax= 1.18628e+03, atom=
> 4303
> Step=   18, Dmax= 3.9e-02 nm, Epot= -7.32653e+04 Fmax= 3.34851e+03, atom=
> 4301
> Step=   19, Dmax= 4.6e-02 nm, Epot= -7.34325e+04 Fmax= 2.54904e+03, atom=
> 4301
> Step=   20, Dmax= 5.5e-02 nm, Epot= -7.35292e+04 Fmax= 2.92387e+03, atom=
> 4301
> Step=   21, Dmax= 6.7e-02 nm, Epot= -7.36418e+04 Fmax= 2.20184e+03, atom=
> 4301
>
>                                         140,1
> .
> .
> .
> .

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================