[gmx-users] Editing the functions of amber

[Asaf Farhi]

Thank you very much for the reply.
I tried to send this question few days ago and they said that I'm not allowed to post there.
(The edition of the replica exchange shouldn't be complicated.) 
Do you have any tips regarding what I should do?

Thanks in advance,
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 5:06 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Editing the functions of amber

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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