On 8/8/19 5:04 PM, Wahl, David M wrote:
Hello,
I am working on parameterizing a small molecule using GROMACS and am having
issues during energy minimization. I want the program to output the potential
energy at every step, except it only prints at the initial step. The program
shows that it takes another 7 steps, although it does not print any additional
energies, as seen below:
Steepest Descents:
Tolerance (Fmax) = 1.00000e+01
Number of steps = 500000
Step Time
0 0.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
1.13615e+00 7.60033e+00 9.76498e+00 1.07286e-02 2.59349e+01
Coulomb-14 LJ (SR) Coulomb (SR) Dih. Rest. Potential
-1.42676e+03 -2.64334e+00 4.22198e+02 2.83276e-03 -9.62758e+02
Pressure (bar)
0.00000e+00
Step Time
1 1.00000
Step Time
2 2.00000
Step Time
3 3.00000
Step Time
4 4.00000
Step Time
5 5.00000
Step Time
6 6.00000
Step Time
7 7.00000
I have also tried changing nstlog, nstcalcenergy, and nstenergy all to 1 in the
mdp file, although this yielded the same result as above. Running mdrun
verbose with the -v flag did not change anything either. I understand that they
may not be printing because the energies are relatively close, but we still
would like it to print all of the energies regardless of how small the
differences.
Any insight/recommendations would be greatly appreciated!
mdrun will not print energies during EM if the energy doesn't change or
increases. If you want different behavior, you will have to change how
the minimizer prints output in src/gromacs/mdrun/minimize.cpp.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
--
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.
