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
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Received on Tue Jan 15 2013 - 08:30:03 PST
