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
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Received on Tue Jan 15 2013 - 11:30:03 PST
