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
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Received on Tue Jan 15 2013 - 13:30:02 PST
