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? Are you willing to cooperate with us on 2?
Thanks Best regards, Asaf ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] 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: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf > of Matthew Zwier [mczw...@gmail.com] > 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<asaf.fa...@weizmann.ac.il> > 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 gmx-users@gromacs.org >> 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 gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists