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 =
157,158,159,160,161,164,166,167,169,170,172,173,174,175,178,179,181,182,183,185,18
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,
540,543,545,546,548,549,551,552,553,554,557,558,560,561,562,564,567,568,569,570,571,572,575,577,57
8,580,581,583,584,588,589,590,594,596,599,
igr2 =
915,916,917,918,919,922,924,925,927,928,930,931,932,933,936,937,940,941,943,946,94
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
9,1330,1333,1335,1336,1338,1339,1341,1342,1346,1347,1348,1350,1351,1352,1354,1357
&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
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Received on Tue Jan 15 2013 - 08:00:02 PST
