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
>
--
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 Tue Jan 15 2013 - 13:00:04 PST
