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
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
