[gmx-users] Editing the functions of amber
Mark.Abraham at anu.edu.au
Thu Mar 22 15:24:59 CET 2012
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.
> 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,
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Matthew Zwier [mczwier at 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.
> Matt Zwier
> On Tue, Mar 20, 2012 at 11:52 AM, Asaf Farhi<asaf.farhi at weizmann.ac.il> wrote:
>> Dear Gromacs User
>> 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,
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