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
>
--
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 - 09:00:05 PST
