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
Received on Tue Jan 15 2013 - 07:30:06 PST
