[gmx-users] energy minimization

Tue Jan 9 17:44:13 CET 2018

On Tue, Jan 9, 2018 at 4:31 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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?

I should study different amino acids one by one in my system.In literature
there is just  one NUMBER density profile scheme reported for all
different( in amino acids) tests. This means that this profile should  not
depend on amino acids and should be token before amino acid is in. it's
rational because as you said amino acid can change the distribution of
water also its number density so different amino acids cause different
changes, am i wrong?
However in literature a few distance above surface is considered (1nm) and
my amino acids are in about 1.7 far from surface ( because i want to do
pulling in next step)but i think it's better to remove it( as i have not
access to file before amino acid is in so i thought maybe it's better to
remove it and do EM and equilibration again). What do you think,sir?
BTW, how can i specify the gmx density to just calculate the specific
distance above surface not whole box (Z dimension) ?

Thank you

>

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
>
> ==================================================
>
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