Re: [gmx-users] Re: Energy minimization output

2008-08-13 Thread Justin A. Lemkul 



[EMAIL PROTECTED] wrote:


This is upto 40 ns after that i am not getting anything like that. I don't
know exactly what it mean and how could i get rid of such messages.I don't
know how to deal with it.


What it means is that you had some nasty contacts between some elements of your 
system and the surrounding water.  If the messages do indeed go away during EM, 
and the potential energy levels off to a reasonable, negative value, then things 
should be fine to proceed.


-Justin



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--


Justin A. Lemkul
Graduate Research Assistant
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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RE: [gmx-users] Re: Energy minimization output

2008-08-13 Thread Kukol, Andreas 
Your output looks like, that you are doing MD simulations, because a time in ps 
is reported. You should do energy minimisation first, use 'integrator = steep' 
in your .mdp file

Andreas

 -Original Message-
 From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
 On Behalf Of [EMAIL PROTECTED]
 Sent: 13 August 2008 10:26
 To: gmx-users@gromacs.org
 Subject: [gmx-users] Re: Energy minimization output

 Hi

 I am doing a 5 peptide simulation.

 I have done energy minimization using this command


 1.grompp -v -f em.mdp -c b4em_sol_mov1.gro -p gnnqqny.top -o em.tpr -nice 19

 2.mdrun -v -s em.tpr -e em.edr -c after_em.gro -o em.trr -g em.log -nice 19


 After energy minimization (steep, 5000 steps, emtol 100) i am getting some
 pdb files referring to different steps of energy minimization as
 outputalong with other standard output. when i checked the em.log file i
 am getting




Step   Time Lambda
  15   15.00.0


 t = 0.015 ps: Water molecule starting at atom 8264 can not be settled.
 Check for bad contacts and/or reduce the timestep.Wrote pdb files with
 previous and current coordinates
Step   Time Lambda
  16   16.00.0

Energies (kJ/mol)
Bond  AngleProper Dih. Ryckaert-Bell.  LJ-14
 9.98333e+041.36695e+041.52668e+031.78607e+034.70247e+03
  Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.  Potential
 2.55150e+033.77075e+05   -3.15610e+05   -2.36704e+041.61864e+05
 Kinetic En.   Total EnergyTemperature Pressure (bar)
 0.0e+000.0e+000.0e+000.0e+00


 t = 0.017 ps: Water molecule starting at atom 15071 can not be settled.
 Check for bad contacts and/or reduce the timestep.Wrote pdb files with
 previous and current coordinates
Step   Time Lambda
  17   17.00.0

Step   Time Lambda
  18   18.00.0

Energies (kJ/mol)
Bond  AngleProper Dih. Ryckaert-Bell.  LJ-14
 9.45661e+041.37081e+041.40906e+031.82338e+033.67231e+03
  Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.  Potential
 2.53132e+033.24723e+05   -3.17639e+05   -2.36512e+041.01143e+05
 Kinetic En.   Total EnergyTemperature Pressure (bar)
 0.0e+000.0e+000.0e+000.0e+00

Step   Time Lambda
  19   19.00.0

Energies (kJ/mol)
Bond  AngleProper Dih. Ryckaert-Bell.  LJ-14
 8.03329e+041.30736e+041.41046e+031.92183e+033.32668e+03
  Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.  Potential
 2.50827e+032.64074e+05   -3.15758e+05   -2.36011e+042.72885e+04
 Kinetic En.   Total EnergyTemperature Pressure (bar)
 0.0e+000.0e+000.0e+000.0e+00

Step   Time Lambda
  20   20.00.0

Energies (kJ/mol)
Bond  AngleProper Dih. Ryckaert-Bell.  LJ-14
 6.75745e+041.25722e+041.34546e+031.92589e+033.23734e+03
  Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.  Potential
 2.47910e+032.34231e+05   -3.18011e+05   -2.35785e+04   -1.82240e+04
 Kinetic En.   Total EnergyTemperature Pressure (bar)
 0.0e+000.0e+000.0e+000.0e+00


 t = 0.021 ps: Water molecule starting at atom 15071 can not be settled.
 Check for bad contacts and/or reduce the timestep.Wrote pdb files with
 previous and current coordinates
Step   Time Lambda
  21   21.00.0

Step   Time Lambda
  22   22.00.0

Energies (kJ/mol)
Bond  AngleProper Dih. Ryckaert-Bell.  LJ-14
 5.69021e+041.19959e+041.30660e+031.92492e+033.11441e+03
  Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.  Potential
 2.47034e+032.13147e+05   -3.18361e+05   -2.35596e+04   -5.10587e+04
 Kinetic En.   Total EnergyTemperature Pressure (bar)
 0.0e+000.0e+000.0e+000.0e+00


 This is upto 40 ns after that i am not getting anything like that. I don't
 know exactly what it mean and how could i get rid of such messages.I don't
 know how to deal with it.

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