[gmx-users] GROMACS/ORCA QMMM
Jose Tusell
jrta1981 at gmail.com
Tue Nov 22 04:02:03 CET 2011
Does anyone know what is going on with the coordinates of the QM
region? Why are they not converted to the correct units? Could
anyone point me to the error?
Thanks
Jose Tusell
On Sun, Nov 20, 2011 at 10:06 PM, Jose Tusell <jrta1981 at gmail.com> wrote:
> Yes. But where does the code go wrong? I'm reading the qm_orca.c
> file but I can't seem to know exactly were the factor of 10 is not
> accounted for. I see the factor of ten when going from gromacs to
> orca in (lines 219 to 221 of qm_orca.c file):
>
> qm->xQM[i][XX]/0.1,
> qm->xQM[i][YY]/0.1,
> qm->xQM[i][ZZ]/0.1);
>
> I just don't know where to look for the factor of 10 in the code.
> Could anyone point me to this?
>
> Thanks,
>
> Jose Tusell
>
> On Sun, Nov 20, 2011 at 10:00 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>> 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 <jrta1981 at 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 <jrta1981 at 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
>>>>> <cri at 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<swatipatel088 at 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<jrta1981 at 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<jalemkul at 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<jalemkul at 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
>>>>>>>>>>>>
>>>>>>>>>>>> ========================================
>>>>>>>>>>>> --
>>>>>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>>>>>>>> Please search the archive at
>>>>>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before
>>>>>>>>>>>> posting!
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>>>>>>>>>>>> interface
>>>>>>>>>>>> or send it to gmx-users-request at gromacs.org.
>>>>>>>>>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> ========================================
>>>>>>>>>>
>>>>>>>>>> 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
>>>>>>>>>>
>>>>>>>>>> ========================================
>>>>>>>>>> --
>>>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>>>>>> Please search the archive at
>>>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>>>>>>>>>> interface
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>>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
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>>>>>>>> --
>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
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>>>>>> --
>>>>>> gmx-users mailing list gmx-users at gromacs.org
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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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