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).
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
