Re: [AMBER] umbrella sampling

From: Ross Walker <ross.rosswalker.co.uk>
Date: Tue, 15 Jan 2013 07:40:21 -0800

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
>> > > > > UniversitÓ 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
>> > > > UniversitÓ 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
>> > UniversitÓ 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
>UniversitÓ 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



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Received on Tue Jan 15 2013 - 08:00:03 PST
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