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
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Received on Tue Jan 15 2013 - 13:00:05 PST
