[gmx-users] Editing the functions of amber

[Asaf Farhi]

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-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.

Cheers,
Matt Zwier

On Tue, Mar 20, 2012 at 11:52 AM, Asaf Farhi <asaf.farhi at 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
>
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