Dear Matt Hopefully last question. Do you know if there's a way to get from replica exchange function energy of e certain group (like bonding energy)? It will make the implementation much easier.
Thanks again, Best regards, Asaf ________________________________________ From: [email protected] [[email protected]] on behalf of Asaf Farhi [[email protected]] Sent: Thursday, March 22, 2012 6:00 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] Editing the functions of amber Thank you very much. Have a nice weekend, Asaf ________________________________________ From: [email protected] [[email protected]] on behalf of Mark Abraham [[email protected]] Sent: Thursday, March 22, 2012 5:59 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Editing the functions of amber On 23/03/2012 2:56 AM, Asaf Farhi wrote: > Thank you very much for the reply. > I tried to send this question few days ago and they said that I'm not allowed > to post there. > (The edition of the replica exchange shouldn't be complicated.) > Do you have any tips regarding what I should do? Read the RE documentation the manual and mdrun -h. Get out a debugger and step through the code. Most of the stuff relevant to replica exchange is in src/kernel/repl_ex.c Mark > > Thanks in advance, > Best regards, > Asaf_ > _______________________________________ > From: [email protected] [[email protected]] on behalf > of Mark Abraham [[email protected]] > Sent: Thursday, March 22, 2012 5:06 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Editing the functions of amber > > On 23/03/2012 1:59 AM, Asaf Farhi wrote: >> Dear Matt >> >> Thank you very much for the reply. >> About 1 - it's cutoff in the energy, meaning that from a certain energy you >> will get this energy. >> Can this be done with the table lookups? > Yes, any potential that is a function of distance between pairs can be > done. See manual 6.7.2. Of course, plain cut-offs can be done without > tables since about 1976... > >> Are you willing to cooperate with us on 2? > I don't have time for new projects, but a post to gmx-developers may > elicit feedback on feasibility. > > Mark > >> Thanks >> Best regards, >> Asaf >> >> ________________________________________ >> From: [email protected] [[email protected]] on >> behalf of Mark Abraham [[email protected]] >> Sent: Thursday, March 22, 2012 4:24 PM >> To: Discussion list for GROMACS users >> Subject: Re: [gmx-users] Editing the functions of amber >> >> On 23/03/2012 12:50 AM, Asaf Farhi wrote: >>> Dear Matt >>> >>> Thank you very much for your reply. >>> The things we want to change are the following: >>> 1. Introduce a cutoff energy in the Van Der Waals and electrical potential. >>> 2. Editing the replica exchange function. >>> 3. Multiplying functions by a factor (mostly the covalent bond and >>> constraints potentials). >> Probably you can do 1 and 3 with table lookups - see manual. >> >> Mark >> >>> In the project we want to calculate free energy of RNAs. We want to run a >>> MD simulation with these changes. We'll be happy to cooperate with you on >>> this project (we hope that it'll lead to an article). >>> >>> Thank you very much, >>> Best regards, >>> Asaf >>> >>> ________________________________________ >>> From: [email protected] [[email protected]] on >>> behalf of Matthew Zwier [[email protected]] >>> Sent: Tuesday, March 20, 2012 8:15 PM >>> To: Discussion list for GROMACS users >>> Subject: Re: [gmx-users] Editing the functions of amber >>> >>> Dear Asaf, >>> >>> I think we need significantly more information in order to help you. >>> What function are you trying to port? What are you trying to do with >>> it (that is, what is the scientific question you're trying to answer)? >>> >>> GROMACS is a clean codebase, and remarkably easy to read for how much >>> computer science goes into it. However, there will likely be a >>> relatively severe impedance mismatch between the AMBER and GROMACS >>> code. AMBER is written primarily in FORTRAN, and GROMACS is written >>> entirely in C. Data (like topology and coordinates) are stored >>> differently in each code. Finally, GROMACS uses a lot of specialized >>> techniques to speed up computations (table lookups instead of function >>> calls, and the like), so implementing an algorithm in GROMACS is often >>> more about re-expressing the algorithm in GROMACS style than it is >>> about simply transliterating a routine from FORTRAN into C. >>> >>> What you're proposing is likely to be almost as formidable a task as >>> implementing an algorithm from scratch based on the original papers. >>> That said, our group has had success with modifying GROMACS code in >>> the past, and it turned out to be an efficient solution. >>> >>> Cheers, >>> Matt Zwier >>> >>> On Tue, Mar 20, 2012 at 11:52 AM, Asaf Farhi<[email protected]> >>> wrote: >>>> Dear Gromacs User >>>> >>>> Hi. >>>> My name is Asaf and I'm trying to edit one of the functions in amber in >>>> order to use it in GROMACS. >>>> I wanted to ask if anyone knows how to do it? >>>> >>>> Thanks in advance, >>>> Best regards, >>>> Asaf >>>> >>>> -- >>>> gmx-users mailing list [email protected] >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>>> Please don't post (un)subscribe requests to the list. Use the >>>> www interface or send it to [email protected]. >>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> -- >>> gmx-users mailing list [email protected] >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to [email protected]. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
