Jose Tusell wrote:
When I run gromacs with bOpt yes I run into the a problem with the
coordinates of my qm system: the initial coordinates are the
following:
NAME = ybu_em_qmmm.inp
| 1> #input-file generated by gromacs
| 2> !QMMMOpt TightSCF
| 3> !PAL8 Quick-DFT VerySlowConv TightSCF KDIIS VDW EnGrad NoUseSym
| 4> %scf
| 5> Maxiter 5000
| 6> end
| 7> %pal nprocs 8
| 8> end
| 9>
| 10>
| 11>
| 12> %LJCOEFFICIENTS "ybu_em_qmmm.LJ"
| 13> *xyz -2 1
| 14> 7 46.4499998 40.2500010 48.1099987
| 15> 6 45.2400017 40.2899981 47.5600004
| 16> 7 44.7599983 40.6899977 46.3600016
| 17> 6 43.4700012 40.5999994 46.0599995
| 18> 7 42.6300001 40.1100016 46.9500017
| 19> 6 43.0100012 39.6799994 48.1699991
| 20> 7 42.1299982 39.1499996 49.0199995
| 21> 1 42.4300003 38.8100004 49.9200010
| 22> 1 41.1600018 39.0899992 48.7699986
| 23> 6 44.3400002 39.7700000 48.4999990
| 24> 7 45.0799990 39.4600010 49.5800018
| 25> 6 46.3500023 39.7600007 49.3499994
| 26> 6 47.7699995 40.5399990 47.4900007
| 27> 8 48.8000011 41.0900021 48.3400011
| 28> 6 49.8199987 41.7100000 47.4800014
| 29> 6 47.7400017 41.5500021 46.3600016
| 30> 8 46.9999981 41.4499998 45.1499987
| 31> 1 47.2300005 40.5999994 44.6799994
| 32> 6 49.1900015 41.9199991 46.1000013
| 33> 8 49.7800016 40.8699989 45.3399992
| 34> 1 50.7399988 41.0900021 45.1599979
| 35> 6 50.0799990 43.2399988 47.5799990
| 36> 8 51.4400005 43.5300016 47.9400015
| 37> 15 51.8400002 43.3099985 49.4799995
| 38> 8 52.1000004 44.8099995 49.9800014
| 39> 8 50.5700016 42.5000000 50.0600004
| 40> 8 53.1099987 42.3299980 49.3599987
| 41> 15 54.4700003 43.1799984 49.4500017
| 42> 8 55.5600023 42.1400023 48.8899994
| 43> 8 54.1200018 44.4799995 48.5599995
| 44> 8 54.5300007 43.5900021 50.9999990
| 45> 15 55.8799982 43.3500004 51.8499994
| 46> 8 57.0900011 43.9900017 50.9899998
| 47> 8 55.8300018 43.9099979 53.2200003
| 48> 8 56.1399984 41.7600012 51.8499994
| 49> 1 43.1099987 40.9200001 45.1000023
| 50> 1 47.1600008 39.6399999 50.0400019
| 51> 1 48.1400013 39.6199989 47.0900011
| 52> 1 47.3199987 42.4200010 46.8200016
| 53> 1 49.3300009 42.8999996 45.7000017
| 54> 1 50.7200003 41.1499977 47.4200010
| 55> 1 49.8600006 43.6999989 46.6300011
| 56> 1 49.4299984 43.6600018 48.3199978
| 57> 12 51.3999987 43.3799982 51.9299984
| 58> *
| 59> %pointcharges "ybu_em_qmmm.pc"
| 60>
| 61>
| 62> ****END OF INPUT****
This first calculation doesn't run into problems however after this
the new coordinates are wrong by a factor of 10.
This is the next input file generated by gromacs:
NAME = ybu_em_qmmm.inp
| 1> #input-file generated by gromacs
| 2> !QMMMOpt TightSCF
| 3> !PAL8 Quick-DFT VerySlowConv TightSCF KDIIS VDW EnGrad NoUseSym
| 4> %scf
| 5> Maxiter 5000
| 6> end
| 7> %pal nprocs 8
| 8> end
| 9>
| 10>
| 11>
| 12> %LJCOEFFICIENTS "ybu_em_qmmm.LJ"
| 13> *xyz -2 1
| 14> 7 4.6643215 4.0067959 4.8652828
| 15> 6 4.4694147 4.0687612 4.6910113
| 16> 7 4.4788954 4.0736303 4.5814043
| 17> 6 4.2882785 4.0960234 4.5192298
| 18> 7 4.1568694 3.9851558 4.6636197
| 19> 6 4.2702511 3.9942223 4.8413402
| 20> 7 4.1388491 3.8647231 4.9325246
| 21> 1 4.2422304 3.8729668 5.0225985
| 22> 1 4.0874949 3.9029175 4.8758829
| 23> 6 4.4479644 3.9264068 4.8907641
| 24> 7 4.4724247 3.8935867 5.0617158
| 25> 6 4.6581322 3.9623603 4.9860328
| 26> 6 4.7224784 3.9516553 4.7729388
| 27> 8 4.9013394 4.1037330 4.9433815
| 28> 6 5.0506485 4.1505158 4.7845429
| 29> 6 4.7479546 4.2596489 4.5867884
| 30> 8 4.6396983 4.1753584 4.3912268
| 31> 1 4.7245148 4.0333679 4.4395000
| 32> 6 4.9467531 4.1628179 4.5303190
| 33> 8 5.0127959 4.0332937 4.4357231
| 34> 1 5.0972128 4.1086709 4.5025694
| 35> 6 4.9707726 4.4155064 4.7358957
| 36> 8 5.1747119 4.3822494 4.7240046
| 37> 15 5.1759595 4.3526104 4.9696961
| 38> 8 5.2000558 4.5951414 5.0385225
| 39> 8 4.9872991 4.2056358 5.0856835
| 40> 8 5.3196424 4.1316289 4.9306369
| 41> 15 5.4781163 4.3365851 4.9144840
| 42> 8 5.6436682 4.1501650 4.8309124
| 43> 8 5.4556131 4.5460758 4.7758737
| 44> 8 5.4388809 4.3959689 5.1872373
| 45> 15 5.6339312 4.3419433 5.2184927
| 46> 8 5.8053279 4.4479111 5.0789297
| 47> 8 5.5981785 4.4297397 5.4245871
| 48> 8 5.6559128 4.0851763 5.2241915
| 49> 1 4.2944524 4.1013804 4.4863331
| 50> 1 4.7380015 3.9515409 5.0357658
| 51> 1 4.8261809 3.9258796 4.7002071
| 52> 1 4.7115117 4.2592505 4.6899751
| 53> 1 4.9388400 4.3221569 4.5484522
| 54> 1 5.1027077 4.0887082 4.7342393
| 55> 1 4.9870053 4.3987840 4.6446544
| 56> 1 4.9254298 4.3886098 4.8489299
| 57> 12 5.1316565 4.3423077 5.2266484
| 58> *
| 59> %pointcharges "ybu_em_qmmm.pc"
| 60>
| 61>
| 62> ****END OF INPUT****
Any ideas why this is happening?
A factor of 10 would seem to me to be an Angstrom -> nm conversion.
-Justin
Thanks,
Jose Tusell
On Sun, Nov 20, 2011 at 5:03 PM, Jose Tusell <jrta1...@gmail.com> wrote:
That solved it. In the ORCA manual for version 2.8 it says to use
bOpt = true instead of bOpt = yes. And there is no mention of the mdp
option in the gromacs manual or gromacs online mdp options.
Ramon
On Sun, Nov 20, 2011 at 4:57 PM, Jose Tusell <jrta1...@gmail.com> wrote:
I've tried the bOpt = true. Is the flag bOpt = yes? I'll try that
and I'll let you know.
Ramon
On Sun, Nov 20, 2011 at 1:19 PM, Christoph Riplinger
<c...@thch.uni-bonn.de> wrote:
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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========================================
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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