Dear Aron,
thank you very much for your suggestion.
This sounds good, and it is one of the way that I would like to try: Now I
have to wonder about.
Elisa
2013/1/15 Aron Broom <broomsday.gmail.com>
> yes, you'd want to use one standard angle, and one torsion angle. If the
> cylinders are imagined to look like:
>
> A'------------B'
> --------X-------
> A"-----------B"
>
> C'-------------D'
> --------Y--------
> C"------------D"
>
> Then you'd have:
>
> Distance: X -> Y, which is your umbrella sampling reaction coordinate
> Torsion: (C or D) -> Y -> X -> (A or B), and then fix this within a range
> accordingly (e.g. if you choose C" -> Y -> X -> B", fix it to 180 degrees
> +/- some amount)
> Angle: C" -> Y -> X, and then fix this accordingly (e.g. for C" -> Y -> X,
> you might also be choosing 0 or 180 degrees)
>
> In this way, the torsion angle is what actually keeps the cylinders
> parallel, and then the standard angle is what stops the now parallel
> cylinders from rotating around one another.
>
> Maybe that's all bogus, it's a lot of geometry.
>
> ~Aron
>
> On Tue, Jan 15, 2013 at 4:00 PM, Elisa Frezza <elisa.frezza.gmail.com
> >wrote:
>
> > Dear Adrian,
> >
> > you are right.
> > When I use only an angular restraint my system are \ / at the end.
> > Now I have to find the second angle for US, but it is not so easy.
> >
> > Thank you very much
> >
> > Elisa
> >
> >
> > 2013/1/15 Adrian Roitberg <roitberg.ufl.edu>
> >
> > > Hi Eliza
> > >
> > > What I mean is that two cilinders can bet like this | |
> > > or like this
> > > \ /
> > >
> > > or one in the plane of the monitor and one NOT in the plane of the
> > > monitor ;-)
> > >
> > > Hence, you need TWO angles to define the relative orientation between
> > > two lines.
> > >
> > > adrian
> > >
> > > On 1/15/13 3:50 PM, Elisa Frezza wrote:
> > > > Dear Adrian,
> > > >
> > > > Thank you very much for your answer and your opinion.
> > > > Perhaps, I can consider only a restraint of distance, but I have to
> > > wonder
> > > > more carefully.
> > > > I would like to ask you what kind of angle restraint do I have to
> use?
> > > What
> > > > do you mean with euler coordinates?
> > > > I think to use torsional restraint, is it right? What do you suggest?
> > > >
> > > > Best regards
> > > >
> > > > Elisa
> > > >
> > > >
> > > >
> > > > 2013/1/15 Adrian Roitberg <roitberg.ufl.edu>
> > > >
> > > >> Hi Eliza
> > > >>
> > > >> in that paper, the y present the PMF between DNA strands by "To this
> > end
> > > >> we added a restraint to the DNA oligomers
> > > >> to bias them to sample the distance between their centers in a range
> > of
> > > >> 22 – 38 °A (smallest and
> > > >> farthest separations, respectively). Several harmonic restraining
> > > >> potentials have been put on both
> > > >> DNA oligomers to ensure their approach in parallel orientation."
> > > >>
> > > >> This is quite simply totally wrong. You CANNOT do such a thing!
> > > >>
> > > >> At best, it would be a cut of a 2-D (or more) dimensional surface,
> > with
> > > >> biases that are not well defined. There is absolutely no reason to
> > > >> believe that the approach between 2 DNA strands has them parallel to
> > > >> each other in a minimum path sort of way.
> > > >>
> > > >> One more thing: to have two cylinders approaching each other in
> space,
> > > >> requires one distance and TWO angles (euler coordinates), not just
> one
> > > >> angle...
> > > >>
> > > >> adrian
> > > >>
> > > >> On 1/15/13 11:56 AM, Elisa Frezza wrote:
> > > >>> Dear Rodrigo,
> > > >>>
> > > >>> I would like to study the PMF of a couple of DNA as reported in
> this
> > > >>> article http://pubs.acs.org/doi/abs/10.1021/ja070207t
> > > >>> I also would like to change the relative angle between the duplex.
> > > >>> I do not care about change in DNA conformation
> > > >>> I hope to have explain better my problem.
> > > >>>
> > > >>> Best regards
> > > >>>
> > > >>> Elisa
> > > >>>
> > > >>>
> > > >>> 2013/1/15 ros <rodrigogalindo.gmail.com>
> > > >>>
> > > >>>> Hello Elisa!
> > > >>>>
> > > >>>> Depending on what you want to learn with your simulation, setting
> up
> > > the
> > > >>>> restraints for a double strand DNA can be very tricky. Consider
> that
> > > if
> > > >> you
> > > >>>> set up more than one restraint, this will result in a multi
> > > dimensional
> > > >>>> sampling which will affect your results, as Prof. Roitberg pointed
> > > out.
> > > >> If
> > > >>>> you are planning to use Prof. Grossfield WHAM implementation, this
> > > code
> > > >>>> will only do 2D sampling decomposition, so, for more than 2
> > restraints
> > > >> you
> > > >>>> will have to write your own code or try to use other sampling
> > > techniques
> > > >>>> like mbar or Plumed.
> > > >>>>
> > > >>>> I am not sure what you are trying to do, but a dodecamer is a huge
> > > >>>> molecule, so I would recommend that you start with a simple base
> > pair
> > > >> and
> > > >>>> try different anchor points for your distance restraints (in my
> > > >> experience,
> > > >>>> C1', O1P, O2P or P are good starting points) and see what works.
> > > >>>>
> > > >>>> Finally, to capture the changes in the PES involving different
> > > >> conformation
> > > >>>> of DNA, I would recommend to use small windows (1 or even 0.5 A)
> > which
> > > >>>> results in a lot of computing time.
> > > >>>>
> > > >>>> Hope that helps!
> > > >>>>
> > > >>>> Rodrigo.
> > > >>>>
> > > >>>>
> > > >>>> On Tue, Jan 15, 2013 at 9:05 AM, Elisa Frezza <
> > elisa.frezza.gmail.com
> > > >>>>> wrote:
> > > >>>>> Dear Ross,
> > > >>>>>
> > > >>>>> Thank you very much.
> > > >>>>>
> > > >>>>> Best regards
> > > >>>>>
> > > >>>>> Elisa
> > > >>>>>
> > > >>>>>
> > > >>>>> 2013/1/15 Ross Walker <ross.rosswalker.co.uk>
> > > >>>>>
> > > >>>>>> Dear Elisa et al,
> > > >>>>>>
> > > >>>>>> Please refer to the following webpage which maintains an up to
> > date
> > > >>>> list
> > > >>>>>> of what is and isn't supported with the GPU code:
> > > >>>>>>
> > > >>>>>> http://ambermd.org/gpus/
> > > >>>>>>
> > > >>>>>> Specifically:
> > > >>>>>>
> > > >>>>>> 12) nmropt = 1 .and. For n=1,4; iat(n) < 0The GPU code does not
> > > >>>> currently
> > > >>>>>> support the use of COM simulations.
> > > >>>>>>
> > > >>>>>>
> > > >>>>>> An update will be coming soon that will add Jarzynski support
> and
> > > GBSA
> > > >>>>>> support (as well as CUDA 5.0 and some additional bug fixes and
> > > >> tweaks).
> > > >>>>>> COM restraints are next on the list to be added but it may take
> a
> > > >>>> while.
> > > >>>>>> Until then I would suggest using pmemd.MPI running on CPUs which
> > > >> should
> > > >>>>>> support center of mass restraints.
> > > >>>>>>
> > > >>>>>> All the best
> > > >>>>>> Ross
> > > >>>>>>
> > > >>>>>>
> > > >>>>>> On 1/15/13 7:32 AM, "Elisa Frezza" <elisa.frezza.gmail.com>
> > wrote:
> > > >>>>>>
> > > >>>>>>> I have tried, but it does not work, perhaps there are some
> > mistakes
> > > >> in
> > > >>>>> my
> > > >>>>>>> restraint file.
> > > >>>>>>> My file is:
> > > >>>>>>> #DNA
> > > >>>>>>> #dna
> > > >>>>>>> &rst iat=-1,-1,
> > > >>>>>>> ninc=0,ir6=0,ifntyp=0,nstep1=1,nstep2=100000,
> > > >>>>>>> r1=0.0000E+00,r2=18.0000,r3=18.0000,r4=100.000,rk2=5,rk3=5,
> > > >>>>>>> igr1 =
> > > >>
> > >
> >
> 157,158,159,160,161,164,166,167,169,170,172,173,174,175,178,179,181,182,18
> > > >>>>>>> 3,185,18
> > > >>
> > >
> >
> 8,189,190,191,192,193,196,198,199,201,202,204,205,209,210,211,213,214,215,
> > > >>>>>>> 217,220,536,537,538,539,
> > > >>
> > >
> >
> 540,543,545,546,548,549,551,552,553,554,557,558,560,561,562,564,567,568,56
> > > >>>>>>> 9,570,571,572,575,577,57
> > > >>>>>>> 8,580,581,583,584,588,589,590,594,596,599,
> > > >>>>>>> igr2 =
> > > >>
> > >
> >
> 915,916,917,918,919,922,924,925,927,928,930,931,932,933,936,937,940,941,94
> > > >>>>>>> 3,946,94
> > > >>
> > >
> >
> 7,948,949,950,951,954,956,957,959,960,962,963,967,968,969,971,972,973,975,
> > > >>>>>>> 978,1294,1295,1296,1297,
> > > >>
> > >
> >
> 1298,1301,1303,1304,1306,1307,1309,1310,1311,1312,1315,1316,1319,1320,1322
> > > >>>>>>> ,1325,1326,1327,1328,132
> > > >>
> > >
> >
> 9,1330,1333,1335,1336,1338,1339,1341,1342,1346,1347,1348,1350,1351,1352,13
> > > >>>>>>> 54,1357
> > > >>>>>>> &end
> > > >>>>>>>
> > > >>>>>>> NOTE: I have not include angular restraint.
> > > >>>>>>>
> > > >>>>>>>
> > > >>>>>>> 2013/1/15 Aron Broom <broomsday.gmail.com>
> > > >>>>>>>
> > > >>>>>>>> is the COM restraint just not supported on GPU then? I was
> > going
> > > to
> > > >>>>> try
> > > >>>>>>>> and apply one myself on the PMEMD GPU version, and I had
> thought
> > > >>>> that
> > > >>>>>>>> was
> > > >>>>>>>> one of the improvement for AMBER12. Have you tested your
> input
> > > file
> > > >>>>>>>> with
> > > >>>>>>>> just PMEMD or even sander and confirmed that it works there
> and
> > > just
> > > >>>>> not
> > > >>>>>>>> with pmemd.cuda?
> > > >>>>>>>>
> > > >>>>>>>> ~Aron
> > > >>>>>>>>
> > > >>>>>>>> On Tue, Jan 15, 2013 at 7:23 AM, Elisa Frezza <
> > > >>>> elisa.frezza.gmail.com
> > > >>>>>>>>> wrote:
> > > >>>>>>>>> Dear Aron,
> > > >>>>>>>>>
> > > >>>>>>>>> thank you very much for your answer. I am using PMEMD GPU in
> > > >>>>> AMBER12,
> > > >>>>>>>> and I
> > > >>>>>>>>> try to use COM restraint but it fails.
> > > >>>>>>>>> It is quite difficult to explain you without a figure what I
> am
> > > >>>>>>>> doing. If
> > > >>>>>>>>> you want, I can write in your private email and I am trying
> to
> > > >>>>> explain
> > > >>>>>>>> you
> > > >>>>>>>>> better.
> > > >>>>>>>>>
> > > >>>>>>>>> Thank you in advance
> > > >>>>>>>>>
> > > >>>>>>>>> Elisa
> > > >>>>>>>>>
> > > >>>>>>>>>
> > > >>>>>>>>> 2013/1/15 Aron Broom <broomsday.gmail.com>
> > > >>>>>>>>>
> > > >>>>>>>>>> 1) I believe you can indeed do a COM restraint (I assume you
> > > >>>> mean
> > > >>>>>>>> the
> > > >>>>>>>>>> distance between multiple atoms center of mass?), it just
> > > >>>> requires
> > > >>>>>>>>> defining
> > > >>>>>>>>>> groups, it should all be in the manual under the NMR
> > refinement
> > > >>>>>>>> section.
> > > >>>>>>>>>> 2) For umbrella sampling, you can define say an angular
> > > >>>> restraint
> > > >>>>>>>> (or
> > > >>>>>>>>>> several) to hold things in the orientation you want and then
> > do
> > > >>>>> the
> > > >>>>>>>>>> umbrella sampling along just a distance. This will work and
> > if
> > > >>>>> not
> > > >>>>>>>>>> uncommon, but you just have to be aware that the PMF you are
> > > >>>>>>>> getting is
> > > >>>>>>>>> for
> > > >>>>>>>>>> that particular movement only. If you have good reason to
> > think
> > > >>>>>>>> that
> > > >>>>>>>> is
> > > >>>>>>>>>> the most energetically relevant movement (i.e. lowest free
> > > >>>> energy
> > > >>>>>>>> path)
> > > >>>>>>>>>> then it is a fair assumption to make.
> > > >>>>>>>>>>
> > > >>>>>>>>>> ~Aron
> > > >>>>>>>>>>
> > > >>>>>>>>>> On Tue, Jan 15, 2013 at 7:11 AM, Elisa Frezza
> > > >>>>>>>> <elisa.frezza.gmail.com
> > > >>>>>>>>>>> wrote:
> > > >>>>>>>>>>> Have you any suggestions?
> > > >>>>>>>>>>>
> > > >>>>>>>>>>>
> > > >>>>>>>>>>> 2013/1/15 Elisa Frezza <elisa.frezza.gmail.com>
> > > >>>>>>>>>>>
> > > >>>>>>>>>>>> Dear Adrian,
> > > >>>>>>>>>>>>
> > > >>>>>>>>>>>> thank you very much for your answer. I am using AMBER12
> and
> > > >>>> I
> > > >>>>> am
> > > >>>>>>>> not
> > > >>>>>>>>>> sure
> > > >>>>>>>>>>>> that I can use COM restraint.
> > > >>>>>>>>>>>> At the same time, if I use only a distance restraint, my
> > > >>>>>>>> molecules
> > > >>>>>>>>>> start
> > > >>>>>>>>>>>> to rotate and they are not parallel each other.
> > > >>>>>>>>>>>>
> > > >>>>>>>>>>>> In conclusion, my question is: Can I put a lot of
> restraints
> > > >>>>> and
> > > >>>>>>>> then
> > > >>>>>>>>>>>> consider only a distance between two atoms or is it not
> > > >>>> right?
> > > >>>>>>>>>>>> Elisa
> > > >>>>>>>>>>>>
> > > >>>>>>>>>>>>
> > > >>>>>>>>>>>> 2013/1/15 Adrian Roitberg <roitberg.ufl.edu>
> > > >>>>>>>>>>>>
> > > >>>>>>>>>>>>> Elisa,
> > > >>>>>>>>>>>>> Look at the Center of Mass restraints in the manual.
> > > >>>>>>>>>>>>>
> > > >>>>>>>>>>>>> Also, if you want distance and angle PMF, you would need
> at
> > > >>>>>>>> least
> > > >>>>>>>> a
> > > >>>>>>>>>> 2-D
> > > >>>>>>>>>>>>> umbrella sampling scheme.
> > > >>>>>>>>>>>>>
> > > >>>>>>>>>>>>> adrian
> > > >>>>>>>>>>>>>
> > > >>>>>>>>>>>>> On 1/15/13 9:12 AM, Elisa Frezza wrote:
> > > >>>>>>>>>>>>>> Dear All,
> > > >>>>>>>>>>>>>>
> > > >>>>>>>>>>>>>> I am doing Umbrella Sampling on a pair of dodecamer and
> I
> > > >>>>>>>> would
> > > >>>>>>>>> like
> > > >>>>>>>>>>> to
> > > >>>>>>>>>>>>>> obtain the PMF as a function of the relative distance
> and
> > > >>>>>>>>>> orientation.
> > > >>>>>>>>>>>>>> I have noticed that I have to use a lot of restrains.
> > > >>>>>>>>>>>>>> My question is:
> > > >>>>>>>>>>>>>> is it right to put the restraint for each bond? Is it
> > > >>>> right
> > > >>>>>>>> to
> > > >>>>>>>>>> obtain
> > > >>>>>>>>>>>>> the
> > > >>>>>>>>>>>>>> PMF?
> > > >>>>>>>>>>>>>>
> > > >>>>>>>>>>>>>> My restraint files is like this:
> > > >>>>>>>>>>>>>>
> > > >>>>>>>>>>>>>>
> > > >>>>>>>>>>>>>> #DNA
> > > >>>>>>>>>>>>>> #dna
> > > >>>>>>>>>>>>>> &rst
> > > >>>>>>>>>>>>>> iat=62,820
> > > >>>>>>>>>>>>>>
> > > >>>>>>>>
> r1=0.0000E+00,r2=28.0000,r3=28.0000,r4=56.000,rk2=5,rk3=5,ir6=0,
> > > >>>>>>>>>>>>>> &end
> > > >>>>>>>>>>>>>> &rst
> > > >>>>>>>>>>>>>> iat=92,850
> > > >>>>>>>>>>>>>>
> > > >>>>>>>>
> r1=0.0000E+00,r2=28.0000,r3=28.0000,r4=56.000,rk2=5,rk3=5,ir6=0,
> > > >>>>>>>>>>>>>> &end
> > > >>>>>>>>>>>>>> &rst
> > > >>>>>>>>>>>>>> iat=125,883
> > > >>>>>>>>>>>>>>
> > > >>>>>>>>
> r1=0.0000E+00,r2=28.0000,r3=28.0000,r4=56.000,rk2=5,rk3=5,ir6=0,
> > > >>>>>>>>>>>>>> &end
> > > >>>>>>>>>>>>>>
> > > >>>>>>>>>>>>>> ......
> > > >>>>>>>>>>>>>>
> > > >>>>>>>>>>>>>> thank you in advance
> > > >>>>>>>>>>>>>>
> > > >>>>>>>>>>>>>> Elisa
> > > >>>>>>>>>>>>>>
> > > >>>>>>>>>>>>> --
> > > >>>>>>>>>>>>> Dr. Adrian E. Roitberg
> > > >>>>>>>>>>>>> Professor
> > > >>>>>>>>>>>>> Quantum Theory Project, Department of
> > > >>>>> Chemistry
> > > >>>>>>>>>>>>> University of Florida
> > > >>>>>>>>>>>>> roitberg.ufl.edu
> > > >>>>>>>>>>>>>
> > > >>>>>>>>>>>>>
> > > >>>>>>>>>>>>> _______________________________________________
> > > >>>>>>>>>>>>> AMBER mailing list
> > > >>>>>>>>>>>>> AMBER.ambermd.org
> > > >>>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>>>>>>>>>>>>
> > > >>>>>>>>>>>>
> > > >>>>>>>>>>>> --
> > > >>>>>>>>>>>> Elisa Frezza
> > > >>>>>>>>>>>> Ph.D. Student in Materials Science and Engineering
> > > >>>>>>>>>>>> Dipartimento di Scienze Chimiche
> > > >>>>>>>>>>>> Università di Padova
> > > >>>>>>>>>>>> via Marzolo, 1
> > > >>>>>>>>>>>> 35131 Padova - Italy
> > > >>>>>>>>>>>> Phone: +39 049 827 5149
> > > >>>>>>>>>>>> Skype: elisa.frezza
> > > >>>>>>>>>>>> Emai: elisa.frezza.gmail.com
> > > >>>>>>>>>>>> elisa.frezza.studenti.unipd.it
> > > >>>>>>>>>>>>
> > > >>>>>>>>>>>>
> > > >>>>>>>>>>>>
> > > >>>>>>>>>>> --
> > > >>>>>>>>>>> Elisa Frezza
> > > >>>>>>>>>>> Ph.D. Student in Materials Science and Engineering
> > > >>>>>>>>>>> Dipartimento di Scienze Chimiche
> > > >>>>>>>>>>> Università di Padova
> > > >>>>>>>>>>> via Marzolo, 1
> > > >>>>>>>>>>> 35131 Padova - Italy
> > > >>>>>>>>>>> Phone: +39 049 827 5149
> > > >>>>>>>>>>> Skype: elisa.frezza
> > > >>>>>>>>>>> Emai: elisa.frezza.gmail.com
> > > >>>>>>>>>>> elisa.frezza.studenti.unipd.it
> > > >>>>>>>>>>> _______________________________________________
> > > >>>>>>>>>>> AMBER mailing list
> > > >>>>>>>>>>> AMBER.ambermd.org
> > > >>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>>>>>>>>>>
> > > >>>>>>>>>>
> > > >>>>>>>>>> --
> > > >>>>>>>>>> Aron Broom M.Sc
> > > >>>>>>>>>> PhD Student
> > > >>>>>>>>>> Department of Chemistry
> > > >>>>>>>>>> University of Waterloo
> > > >>>>>>>>>> _______________________________________________
> > > >>>>>>>>>> AMBER mailing list
> > > >>>>>>>>>> AMBER.ambermd.org
> > > >>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>>>>>>>>>
> > > >>>>>>>>>
> > > >>>>>>>>> --
> > > >>>>>>>>> Elisa Frezza
> > > >>>>>>>>> Ph.D. Student in Materials Science and Engineering
> > > >>>>>>>>> Dipartimento di Scienze Chimiche
> > > >>>>>>>>> Università di Padova
> > > >>>>>>>>> via Marzolo, 1
> > > >>>>>>>>> 35131 Padova - Italy
> > > >>>>>>>>> Phone: +39 049 827 5149
> > > >>>>>>>>> Skype: elisa.frezza
> > > >>>>>>>>> Emai: elisa.frezza.gmail.com
> > > >>>>>>>>> elisa.frezza.studenti.unipd.it
> > > >>>>>>>>> _______________________________________________
> > > >>>>>>>>> AMBER mailing list
> > > >>>>>>>>> AMBER.ambermd.org
> > > >>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>>>>>>>>
> > > >>>>>>>>
> > > >>>>>>>> --
> > > >>>>>>>> Aron Broom M.Sc
> > > >>>>>>>> PhD Student
> > > >>>>>>>> Department of Chemistry
> > > >>>>>>>> University of Waterloo
> > > >>>>>>>> _______________________________________________
> > > >>>>>>>> AMBER mailing list
> > > >>>>>>>> AMBER.ambermd.org
> > > >>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>>>>>>>
> > > >>>>>>>
> > > >>>>>>> --
> > > >>>>>>> Elisa Frezza
> > > >>>>>>> Ph.D. Student in Materials Science and Engineering
> > > >>>>>>> Dipartimento di Scienze Chimiche
> > > >>>>>>> Università di Padova
> > > >>>>>>> via Marzolo, 1
> > > >>>>>>> 35131 Padova - Italy
> > > >>>>>>> Phone: +39 049 827 5149
> > > >>>>>>> Skype: elisa.frezza
> > > >>>>>>> Emai: elisa.frezza.gmail.com
> > > >>>>>>> elisa.frezza.studenti.unipd.it
> > > >>>>>>> _______________________________________________
> > > >>>>>>> AMBER mailing list
> > > >>>>>>> AMBER.ambermd.org
> > > >>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>>>>>
> > > >>>>>> _______________________________________________
> > > >>>>>> AMBER mailing list
> > > >>>>>> AMBER.ambermd.org
> > > >>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>>>>>
> > > >>>>>
> > > >>>>> --
> > > >>>>> Elisa Frezza
> > > >>>>> Ph.D. Student in Materials Science and Engineering
> > > >>>>> Dipartimento di Scienze Chimiche
> > > >>>>> Università di Padova
> > > >>>>> via Marzolo, 1
> > > >>>>> 35131 Padova - Italy
> > > >>>>> Phone: +39 049 827 5149
> > > >>>>> Skype: elisa.frezza
> > > >>>>> Emai: elisa.frezza.gmail.com
> > > >>>>> elisa.frezza.studenti.unipd.it
> > > >>>>> _______________________________________________
> > > >>>>> AMBER mailing list
> > > >>>>> AMBER.ambermd.org
> > > >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>>>>
> > > >>>> _______________________________________________
> > > >>>> AMBER mailing list
> > > >>>> AMBER.ambermd.org
> > > >>>> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>>>
> > > >>>
> > > >> --
> > > >> Dr. Adrian E. Roitberg
> > > >> Professor
> > > >> Quantum Theory Project, Department of Chemistry
> > > >> University of Florida
> > > >> roitberg.ufl.edu
> > > >>
> > > >>
> > > >> _______________________________________________
> > > >> AMBER mailing list
> > > >> AMBER.ambermd.org
> > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>
> > > >
> > > >
> > >
> > > --
> > > Dr. Adrian E. Roitberg
> > > Professor
> > > Quantum Theory Project, Department of Chemistry
> > > University of Florida
> > > roitberg.ufl.edu
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Elisa Frezza
> > Ph.D. Student in Materials Science and Engineering
> > Dipartimento di Scienze Chimiche
> > Università di Padova
> > via Marzolo, 1
> > 35131 Padova - Italy
> > Phone: +39 049 827 5149
> > Skype: elisa.frezza
> > Emai: elisa.frezza.gmail.com
> > elisa.frezza.studenti.unipd.it
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Elisa Frezza
Ph.D. Student in Materials Science and Engineering
Dipartimento di Scienze Chimiche
Università di Padova
via Marzolo, 1
35131 Padova - Italy
Phone: +39 049 827 5149
Skype: elisa.frezza
Emai: elisa.frezza.gmail.com
elisa.frezza.studenti.unipd.it
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Received on Wed Jan 16 2013 - 02:00:03 PST
