[gmx-users] Editing the functions of amber

[Asaf Farhi]

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-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Mark Abraham [Mark.Abraham at 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-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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