Jose Tusell wrote:
Hi Justin,
Thanks for the input on why this is happening. It sounds a little
suspicious that the energy doesn't change after a few steps of energy
minimization. Do you know of any way that I can find out what is
going on?
The screen output should indicate the atom with maximal force. Sometimes the EM
algorithms get stuck when the geometry cannot change without making detrimental
moves. You either need a larger step size, a different algorithm, or a better
starting structure, if that is the case. I have seen this many times before,
nothing suspicious about it.
-Justin
Thanks,
Jose Tusell
On Thu, Nov 17, 2011 at 10:58 AM, Justin A. Lemkul <jalem...@vt.edu> wrote:
Jose Tusell wrote:
Hi Cristoph,
Thanks for the reply. I found that my problem was not gromacs. The
input that ORCA was receiving from GROMACS did not have the correct
number of hydrogens. I've solved this problem now and ORCA is running
fine. I however ran into another problem with my energy minimization.
The output from my gromacs log file is the following:
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
1.21899e+04 1.92496e+03 5.62567e+03 1.49141e+01 3.68001e+03
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum En.
2.41200e+04 1.47494e+05 -5.06544e+05 -7.56009e+04 -3.96508e+06
Potential Pressure (bar)
-4.35218e+06 -2.10629e+04
Step Time Lambda
1 1.00000 0.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
1.20006e+04 1.92297e+03 5.62600e+03 1.47801e+01 3.67746e+03
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum En.
2.41174e+04 1.46421e+05 -5.06609e+05 -7.56156e+04 -4.00402e+06
Potential Pressure (bar)
-4.39246e+06 -2.10739e+04
Step Time Lambda
2 2.00000 0.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
1.17961e+04 1.92126e+03 5.62633e+03 1.46477e+01 3.67461e+03
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum En.
2.41145e+04 1.45528e+05 -5.06679e+05 -7.56315e+04 -4.18671e+06
Potential Pressure (bar)
-4.57635e+06 -2.10854e+04
Step Time Lambda
3 3.00000 0.00000
Step Time Lambda
4 4.00000 0.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
1.16705e+04 1.92041e+03 5.62652e+03 1.45728e+01 3.67282e+03
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum En.
2.41128e+04 1.45113e+05 -5.06721e+05 -7.56410e+04 -4.24486e+06
Potential Pressure (bar)
-4.63509e+06 -2.10913e+04
Step Time Lambda
5 5.00000 0.00000
Step Time Lambda
6 6.00000 0.00000
Step Time Lambda
7 7.00000 0.00000
Step Time Lambda
8 8.00000 0.00000
Step Time Lambda
9 9.00000 0.00000
Step Time Lambda
10 10.00000 0.00000
Step Time Lambda
11 11.00000 0.00000
Step Time Lambda
12 12.00000 0.00000
Step Time Lambda
13 13.00000 0.00000
Step Time Lambda
14 14.00000 0.00000
Step Time Lambda
15 15.00000 0.00000
Step Time Lambda
16 16.00000 0.00000
Step Time Lambda
17 17.00000 0.00000
Step Time Lambda
18 18.00000 0.00000
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000
Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
Why doesn't GROMACS output the energies for certain steps? Step 3 and
steps 5-18 do show any output in the log file. Any ideas why this is
happening?
This happens for the reasons printed by mdrun - those steps caused no change
in energy.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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