[gmx-users] Editing the functions of amber

[Mark Abraham]

On 23/03/2012 1:59 AM, Asaf Farhi wrote:
> 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?

Yes, any potential that is a function of distance between pairs can be 
done. See manual 6.7.2. Of course, plain cut-offs can be done without 
tables since about 1976...

> Are you willing to cooperate with us on 2?

I don't have time for new projects, but a post to gmx-developers may 
elicit feedback on feasibility.

Mark

>
> 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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