Dear Justin,
The LJ and LJ.Excl files should be generated when you set bOpt = yes.
What does the .inp file say. Is there !QMMMOpt or only !EnGrad?
Christoph
On 11/18/2011 06:20 PM, Jose Tusell wrote:
Hi Justin,
I tried using a larger step size but my system blew up... My guess is
that I have a bad starting structure, I'll work on the initial
structure for the QM region (energy minimize).
When I'm running ORCA I want to have a LJ file to correct for the
interaction of my QM system with the protein. However this file is
not created when I run QMMM, I've used the bOpt = true in the mdp
file. Can anyone please offer some help on how to create this LJ
files?
Thanks,
Jose Tusell
On Thu, Nov 17, 2011 at 2:07 PM, swati patel<swatipatel...@gmail.com> wrote:
hello,
I am trying to simulate streptavidin tetramer-biotin complex.I ve calculated
Ligand topology from a sofware PRODRG using gromos87 force fields.After
solvating it,I am getting an error using grompp command
Fatal error:
Atomtype HW not found
can anyone provide me some help?
Thanx with anticipation.
On Fri, Nov 18, 2011 at 2:29 AM, Jose Tusell<jrta1...@gmail.com> wrote:
I'll try changing the step size first and if that fails I'll try
another algorithm. Thanks for the input.
Jose Tusell
On Thu, Nov 17, 2011 at 11:48 AM, Justin A. Lemkul<jalem...@vt.edu>
wrote:
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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